/usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_11A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_11A.pep.xml' '20161205_Sample_11A.pep.xml' -L'7'" file 1: 20161205_Sample_11A.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_11A.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_11A.mzXML in msms_run_summary tag ... processed altogether 94326 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_11A.pep.xml command completed in 39 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_11A.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_11A.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 12 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_11A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 44720 2+, 36857 3+, 8743 4+, 1788 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 24260 Decoys, and 67848 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 60 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_11A.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_11A.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_11A (Comet)"... => Found 36264 hits. (0 decoys, 0 excluded) => Total so far: 36264 hits. (0 decoys, 0 excluded) command completed in 5 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_11A.pep.xml" command completed in 4 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_11A.pep.xml' 'interact-20161205_Sample_11A.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_11A.pep.xml... ...read in 0 1+, 20316 2+, 13129 3+, 2539 4+, 280 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 28123 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 9232 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10407 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10407 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10407 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10407 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10407 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10407 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6792 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10407 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.26997e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_11A.prot.xml command completed in 73 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_11A.prot.xml" Analyzing interact-20161205_Sample_11A.prot.xml ... command completed in 0 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_11A.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_11A.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_11A... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 10:19:44 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_11A.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_11A.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 10:19:49 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_11A.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_11A.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 10:19:49 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_11A.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_11A.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 10:19:49 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_11A.pep.xml' '20161205_Sample_11A.pep.xml' -L'7' 39 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_11A.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_11A.pep.xml' 'Cg-Giga_cont_AA.fa' 12 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_11A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 60 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_11A.pep.xml -d "DECOY_" 5 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_11A.pep.xml 4 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_11A.pep.xml' 'interact-20161205_Sample_11A.prot.xml' 73 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_11A.prot.xml 0 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_11A.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_11A.prot.xml' 0 sec job completed in 198 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_11.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_11.pep.xml' '20161205_Sample_11.pep.xml' -L'7'" file 1: 20161205_Sample_11.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_11.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_11.mzXML in msms_run_summary tag ... processed altogether 94172 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_11.pep.xml command completed in 40 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_11.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_11.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 12 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_11.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 43430 2+, 37127 3+, 9339 4+, 1888 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 24198 Decoys, and 67586 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 60 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_11.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_11.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_11 (Comet)"... => Found 36044 hits. (0 decoys, 0 excluded) => Total so far: 36044 hits. (0 decoys, 0 excluded) command completed in 4 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_11.pep.xml" command completed in 3 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_11.pep.xml' 'interact-20161205_Sample_11.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_11.pep.xml... ...read in 0 1+, 19797 2+, 13375 3+, 2606 4+, 266 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 27910 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 9088 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10283 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10283 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10283 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10283 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10283 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10283 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6736 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10283 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.23024e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_11.prot.xml command completed in 69 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_11.prot.xml" Analyzing interact-20161205_Sample_11.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_11.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_11.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_11... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 10:22:58 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_11.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_11.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 10:23:03 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_11.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_11.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 10:23:03 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_11.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_11.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 10:23:03 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_11.pep.xml' '20161205_Sample_11.pep.xml' -L'7' 40 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_11.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_11.pep.xml' 'Cg-Giga_cont_AA.fa' 12 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_11.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 60 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_11.pep.xml -d "DECOY_" 4 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_11.pep.xml 3 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_11.pep.xml' 'interact-20161205_Sample_11.prot.xml' 69 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_11.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_11.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_11.prot.xml' 0 sec job completed in 194 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_12A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_12A.pep.xml' '20161205_Sample_12A.pep.xml' -L'7'" file 1: 20161205_Sample_12A.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_12A.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_12A.mzXML in msms_run_summary tag ... processed altogether 97212 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_12A.pep.xml command completed in 40 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_12A.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_12A.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 12 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_12A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 46658 2+, 37909 3+, 8624 4+, 1888 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 23600 Decoys, and 71479 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 62 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_12A.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_12A.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_12A (Comet)"... => Found 40385 hits. (0 decoys, 0 excluded) => Total so far: 40385 hits. (0 decoys, 0 excluded) command completed in 5 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_12A.pep.xml" command completed in 4 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_12A.pep.xml' 'interact-20161205_Sample_12A.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_12A.pep.xml... ...read in 0 1+, 22888 2+, 14399 3+, 2753 4+, 345 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 31135 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 9715 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10935 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10935 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10935 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10935 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10935 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10935 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 7236 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10935 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.56119e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_12A.prot.xml command completed in 83 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_12A.prot.xml" Analyzing interact-20161205_Sample_12A.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_12A.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_12A.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_12A... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 10:26:30 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_12A.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_12A.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 10:26:35 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_12A.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_12A.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 10:26:35 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_12A.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_12A.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 10:26:35 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_12A.pep.xml' '20161205_Sample_12A.pep.xml' -L'7' 40 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_12A.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_12A.pep.xml' 'Cg-Giga_cont_AA.fa' 12 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_12A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 62 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_12A.pep.xml -d "DECOY_" 5 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_12A.pep.xml 4 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_12A.pep.xml' 'interact-20161205_Sample_12A.prot.xml' 83 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_12A.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_12A.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_12A.prot.xml' 0 sec job completed in 212 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_12.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_12.pep.xml' '20161205_Sample_12.pep.xml' -L'7'" file 1: 20161205_Sample_12.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_12.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_12.mzXML in msms_run_summary tag ... processed altogether 97734 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_12.pep.xml command completed in 42 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_12.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_12.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 11 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_12.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 45383 2+, 38104 3+, 9606 4+, 2193 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 23385 Decoys, and 71901 Non-Decoys Iterations: .........10.........20....... model complete after 28 iterations command completed in 65 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_12.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_12.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_12 (Comet)"... => Found 41026 hits. (0 decoys, 0 excluded) => Total so far: 41026 hits. (0 decoys, 0 excluded) command completed in 4 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_12.pep.xml" command completed in 4 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_12.pep.xml' 'interact-20161205_Sample_12.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_12.pep.xml... ...read in 0 1+, 22738 2+, 14856 3+, 3070 4+, 362 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 31336 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 9726 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10958 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10958 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10958 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10958 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10958 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10958 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 7249 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10958 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=7.03042e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_12.prot.xml command completed in 84 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_12.prot.xml" Analyzing interact-20161205_Sample_12.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_12.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_12.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_12... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 10:30:06 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_12.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_12.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 10:30:11 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_12.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_12.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 10:30:11 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_12.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_12.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 10:30:11 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_12.pep.xml' '20161205_Sample_12.pep.xml' -L'7' 42 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_12.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_12.pep.xml' 'Cg-Giga_cont_AA.fa' 11 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_12.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 65 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_12.pep.xml -d "DECOY_" 4 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_12.pep.xml 4 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_12.pep.xml' 'interact-20161205_Sample_12.prot.xml' 84 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_12.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_12.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_12.prot.xml' 0 sec job completed in 216 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_16A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_16A.pep.xml' '20161205_Sample_16A.pep.xml' -L'7'" file 1: 20161205_Sample_16A.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_16A.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_16A.mzXML in msms_run_summary tag ... processed altogether 97251 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_16A.pep.xml command completed in 42 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_16A.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_16A.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 12 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_16A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 48593 2+, 36211 3+, 8138 4+, 1994 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 25749 Decoys, and 69187 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 62 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_16A.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_16A.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_16A (Comet)"... => Found 35518 hits. (0 decoys, 0 excluded) => Total so far: 35518 hits. (0 decoys, 0 excluded) command completed in 4 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_16A.pep.xml" command completed in 3 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_16A.pep.xml' 'interact-20161205_Sample_16A.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_16A.pep.xml... ...read in 0 1+, 20598 2+, 12374 3+, 2286 4+, 260 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 27402 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 8951 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10126 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10126 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10126 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10126 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10126 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10126 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6576 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10126 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=5.71297e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_16A.prot.xml command completed in 65 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_16A.prot.xml" Analyzing interact-20161205_Sample_16A.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_16A.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_16A.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_16A... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 10:33:20 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_16A.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_16A.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 10:33:25 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_16A.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_16A.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 10:33:25 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_16A.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_16A.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 10:33:25 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_16A.pep.xml' '20161205_Sample_16A.pep.xml' -L'7' 42 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_16A.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_16A.pep.xml' 'Cg-Giga_cont_AA.fa' 12 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_16A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 62 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_16A.pep.xml -d "DECOY_" 4 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_16A.pep.xml 3 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_16A.pep.xml' 'interact-20161205_Sample_16A.prot.xml' 65 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_16A.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_16A.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_16A.prot.xml' 0 sec job completed in 194 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_16.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_16.pep.xml' '20161205_Sample_16.pep.xml' -L'7'" file 1: 20161205_Sample_16.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_16.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_16.mzXML in msms_run_summary tag ... processed altogether 98031 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_16.pep.xml command completed in 42 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_16.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_16.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 12 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_16.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 48949 2+, 35943 3+, 8554 4+, 2171 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 25823 Decoys, and 69794 Non-Decoys Iterations: .........10.........20....... model complete after 28 iterations command completed in 64 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_16.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_16.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_16 (Comet)"... => Found 36850 hits. (0 decoys, 0 excluded) => Total so far: 36850 hits. (0 decoys, 0 excluded) command completed in 5 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_16.pep.xml" command completed in 3 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_16.pep.xml' 'interact-20161205_Sample_16.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_16.pep.xml... ...read in 0 1+, 21550 2+, 12677 3+, 2371 4+, 252 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 27954 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 9230 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10438 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10438 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10438 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10438 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10438 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10438 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6794 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10438 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.26512e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_16.prot.xml command completed in 73 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_16.prot.xml" Analyzing interact-20161205_Sample_16.prot.xml ... command completed in 0 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_16.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_16.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_16... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 10:36:44 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_16.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_16.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 10:36:49 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_16.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_16.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 10:36:49 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_16.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_16.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 10:36:49 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_16.pep.xml' '20161205_Sample_16.pep.xml' -L'7' 42 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_16.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_16.pep.xml' 'Cg-Giga_cont_AA.fa' 12 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_16.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 64 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_16.pep.xml -d "DECOY_" 5 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_16.pep.xml 3 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_16.pep.xml' 'interact-20161205_Sample_16.prot.xml' 73 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_16.prot.xml 0 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_16.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_16.prot.xml' 0 sec job completed in 204 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_19A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_19A.pep.xml' '20161205_Sample_19A.pep.xml' -L'7'" file 1: 20161205_Sample_19A.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_19A.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_19A.mzXML in msms_run_summary tag ... processed altogether 96676 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_19A.pep.xml command completed in 42 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_19A.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_19A.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 11 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_19A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 47789 2+, 36675 3+, 8241 4+, 1684 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 23870 Decoys, and 70519 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 62 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_19A.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_19A.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_19A (Comet)"... => Found 39389 hits. (0 decoys, 0 excluded) => Total so far: 39389 hits. (0 decoys, 0 excluded) command completed in 5 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_19A.pep.xml" command completed in 3 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_19A.pep.xml' 'interact-20161205_Sample_19A.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_19A.pep.xml... ...read in 0 1+, 22867 2+, 13746 3+, 2482 4+, 294 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 30678 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 9771 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 11024 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 11024 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 11024 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 11024 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 11024 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 11024 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 11024 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 7170 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 11024 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.80245e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_19A.prot.xml command completed in 83 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_19A.prot.xml" Analyzing interact-20161205_Sample_19A.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_19A.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_19A.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_19A... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 10:40:16 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_19A.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_19A.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 10:40:21 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_19A.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_19A.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 10:40:21 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_19A.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_19A.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 10:40:21 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_19A.pep.xml' '20161205_Sample_19A.pep.xml' -L'7' 42 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_19A.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_19A.pep.xml' 'Cg-Giga_cont_AA.fa' 11 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_19A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 62 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_19A.pep.xml -d "DECOY_" 5 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_19A.pep.xml 3 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_19A.pep.xml' 'interact-20161205_Sample_19A.prot.xml' 83 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_19A.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_19A.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_19A.prot.xml' 0 sec job completed in 212 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_19.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_19.pep.xml' '20161205_Sample_19.pep.xml' -L'7'" file 1: 20161205_Sample_19.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_19.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_19.mzXML in msms_run_summary tag ... processed altogether 96696 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_19.pep.xml command completed in 41 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_19.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_19.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 12 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_19.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 45776 2+, 37507 3+, 8772 4+, 2074 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 23876 Decoys, and 70253 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 62 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_19.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_19.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_19 (Comet)"... => Found 38532 hits. (0 decoys, 0 excluded) => Total so far: 38532 hits. (0 decoys, 0 excluded) command completed in 4 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_19.pep.xml" command completed in 4 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_19.pep.xml' 'interact-20161205_Sample_19.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_19.pep.xml... ...read in 0 1+, 21616 2+, 13927 3+, 2671 4+, 318 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 29713 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 9267 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10467 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10467 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10467 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10467 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10467 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10467 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6944 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10467 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.36176e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_19.prot.xml command completed in 77 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_19.prot.xml" Analyzing interact-20161205_Sample_19.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_19.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_19.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_19... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 10:43:42 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_19.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_19.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 10:43:47 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_19.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_19.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 10:43:47 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_19.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_19.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 10:43:47 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_19.pep.xml' '20161205_Sample_19.pep.xml' -L'7' 41 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_19.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_19.pep.xml' 'Cg-Giga_cont_AA.fa' 12 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_19.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 62 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_19.pep.xml -d "DECOY_" 4 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_19.pep.xml 4 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_19.pep.xml' 'interact-20161205_Sample_19.prot.xml' 77 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_19.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_19.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_19.prot.xml' 0 sec job completed in 206 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_1A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_1A.pep.xml' '20161205_Sample_1A.pep.xml' -L'7'" file 1: 20161205_Sample_1A.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_1A.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_1A.mzXML in msms_run_summary tag ... processed altogether 88832 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_1A.pep.xml command completed in 38 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_1A.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_1A.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 11 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_1A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 40726 2+, 35650 3+, 8460 4+, 1905 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 20638 Decoys, and 66103 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 57 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_1A.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_1A.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_1A (Comet)"... => Found 38786 hits. (0 decoys, 0 excluded) => Total so far: 38786 hits. (0 decoys, 0 excluded) command completed in 5 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_1A.pep.xml" command completed in 3 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_1A.pep.xml' 'interact-20161205_Sample_1A.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_1A.pep.xml... ...read in 0 1+, 21296 2+, 14386 3+, 2767 4+, 337 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 30559 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 9866 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 11145 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 11145 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 11145 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 11145 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 11145 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 11145 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 11145 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 7333 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 11145 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.43331e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_1A.prot.xml command completed in 83 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_1A.prot.xml" Analyzing interact-20161205_Sample_1A.prot.xml ... command completed in 0 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_1A.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_1A.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_1A... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 10:47:04 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_1A.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_1A.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 10:47:10 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 6 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_1A.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_1A.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 10:47:10 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_1A.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_1A.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 10:47:10 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_1A.pep.xml' '20161205_Sample_1A.pep.xml' -L'7' 38 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_1A.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_1A.pep.xml' 'Cg-Giga_cont_AA.fa' 11 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_1A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 57 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_1A.pep.xml -d "DECOY_" 5 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_1A.pep.xml 3 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_1A.pep.xml' 'interact-20161205_Sample_1A.prot.xml' 83 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_1A.prot.xml 0 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_1A.pep.xml' 6 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_1A.prot.xml' 0 sec job completed in 203 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_sample_1.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_sample_1.pep.xml' '20161205_sample_1.pep.xml' -L'7'" file 1: 20161205_sample_1.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_sample_1.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_sample_1.mzXML in msms_run_summary tag ... processed altogether 89352 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_sample_1.pep.xml command completed in 38 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_sample_1.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_sample_1.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 11 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_sample_1.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 38850 2+, 36561 3+, 9548 4+, 1969 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 20718 Decoys, and 66210 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 57 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_sample_1.pep.xml -d "DECOY_"" Analyzing interact-20161205_sample_1.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_sample_1 (Comet)"... => Found 38559 hits. (0 decoys, 0 excluded) => Total so far: 38559 hits. (0 decoys, 0 excluded) command completed in 5 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_sample_1.pep.xml" command completed in 3 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_sample_1.pep.xml' 'interact-20161205_sample_1.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_sample_1.pep.xml... ...read in 0 1+, 20196 2+, 14992 3+, 3059 4+, 312 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 29526 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 9601 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10869 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10869 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10869 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10869 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10869 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10869 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 7049 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10869 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.46199e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_sample_1.prot.xml command completed in 79 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_sample_1.prot.xml" Analyzing interact-20161205_sample_1.prot.xml ... command completed in 0 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_sample_1.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_sample_1.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_sample_1... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 10:50:23 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_sample_1.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_sample_1.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 10:50:28 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_sample_1.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_sample_1.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 10:50:29 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_sample_1.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_sample_1.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 10:50:29 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 1 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_sample_1.pep.xml' '20161205_sample_1.pep.xml' -L'7' 38 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_sample_1.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_sample_1.pep.xml' 'Cg-Giga_cont_AA.fa' 11 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_sample_1.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 57 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_sample_1.pep.xml -d "DECOY_" 5 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_sample_1.pep.xml 3 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_sample_1.pep.xml' 'interact-20161205_sample_1.prot.xml' 79 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_sample_1.prot.xml 0 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_sample_1.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_sample_1.prot.xml' 1 sec job completed in 199 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_20A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_20A.pep.xml' '20161205_Sample_20A.pep.xml' -L'7'" file 1: 20161205_Sample_20A.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_20A.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_20A.mzXML in msms_run_summary tag ... processed altogether 95228 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_20A.pep.xml command completed in 41 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_20A.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_20A.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 12 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_20A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 46465 2+, 36514 3+, 8199 4+, 1830 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 23377 Decoys, and 69631 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 60 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_20A.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_20A.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_20A (Comet)"... => Found 38722 hits. (0 decoys, 0 excluded) => Total so far: 38722 hits. (0 decoys, 0 excluded) command completed in 5 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_20A.pep.xml" command completed in 3 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_20A.pep.xml' 'interact-20161205_Sample_20A.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_20A.pep.xml... ...read in 0 1+, 22295 2+, 13628 3+, 2507 4+, 292 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 30137 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 9480 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10721 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10721 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10721 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10721 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10721 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10721 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 7044 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10721 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.25298e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_20A.prot.xml command completed in 75 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_20A.prot.xml" Analyzing interact-20161205_Sample_20A.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_20A.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_20A.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_20A... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 10:53:46 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_20A.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_20A.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 10:53:51 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_20A.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_20A.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 10:53:51 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_20A.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_20A.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 10:53:51 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_20A.pep.xml' '20161205_Sample_20A.pep.xml' -L'7' 41 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_20A.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_20A.pep.xml' 'Cg-Giga_cont_AA.fa' 12 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_20A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 60 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_20A.pep.xml -d "DECOY_" 5 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_20A.pep.xml 3 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_20A.pep.xml' 'interact-20161205_Sample_20A.prot.xml' 75 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_20A.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_20A.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_20A.prot.xml' 0 sec job completed in 202 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_20.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_20.pep.xml' '20161205_Sample_20.pep.xml' -L'7'" file 1: 20161205_Sample_20.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_20.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_20.mzXML in msms_run_summary tag ... processed altogether 96024 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_20.pep.xml command completed in 41 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_20.pep.xml'" command completed in 1 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_20.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 11 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_20.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 45260 2+, 37291 3+, 8911 4+, 2103 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 23326 Decoys, and 70239 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 61 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_20.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_20.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_20 (Comet)"... => Found 39081 hits. (0 decoys, 0 excluded) => Total so far: 39081 hits. (0 decoys, 0 excluded) command completed in 5 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_20.pep.xml" command completed in 3 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_20.pep.xml' 'interact-20161205_Sample_20.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_20.pep.xml... ...read in 0 1+, 21841 2+, 14190 3+, 2745 4+, 305 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 30033 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 9490 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10714 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10714 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10714 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10714 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10714 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10714 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6954 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10714 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.72818e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_20.prot.xml command completed in 78 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_20.prot.xml" Analyzing interact-20161205_Sample_20.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_20.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_20.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_20... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 10:57:12 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_20.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_20.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 10:57:17 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_20.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_20.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 10:57:17 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_20.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_20.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 10:57:17 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_20.pep.xml' '20161205_Sample_20.pep.xml' -L'7' 41 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_20.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_20.pep.xml' 'Cg-Giga_cont_AA.fa' 11 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_20.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 61 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_20.pep.xml -d "DECOY_" 5 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_20.pep.xml 3 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_20.pep.xml' 'interact-20161205_Sample_20.prot.xml' 78 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_20.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_20.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_20.prot.xml' 0 sec job completed in 206 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_24A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_24A.pep.xml' '20161205_Sample_24A.pep.xml' -L'7'" file 1: 20161205_Sample_24A.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_24A.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_24A.mzXML in msms_run_summary tag ... processed altogether 98362 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_24A.pep.xml command completed in 43 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_24A.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_24A.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 12 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_24A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 51761 2+, 35351 3+, 7260 4+, 1722 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 28255 Decoys, and 67839 Non-Decoys Iterations: .........10.........20....... model complete after 28 iterations command completed in 63 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_24A.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_24A.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_24A (Comet)"... => Found 32264 hits. (0 decoys, 0 excluded) => Total so far: 32264 hits. (0 decoys, 0 excluded) command completed in 4 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_24A.pep.xml" command completed in 3 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_24A.pep.xml' 'interact-20161205_Sample_24A.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_24A.pep.xml... ...read in 0 1+, 19792 2+, 10556 3+, 1728 4+, 188 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 25324 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 8917 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10132 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10132 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10132 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10132 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10132 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10132 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6488 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10132 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=5.66241e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_24A.prot.xml command completed in 63 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_24A.prot.xml" Analyzing interact-20161205_Sample_24A.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_24A.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_24A.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_24A... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 11:00:26 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_24A.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_24A.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 11:00:30 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 4 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_24A.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_24A.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 11:00:30 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_24A.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_24A.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 11:00:30 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_24A.pep.xml' '20161205_Sample_24A.pep.xml' -L'7' 43 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_24A.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_24A.pep.xml' 'Cg-Giga_cont_AA.fa' 12 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_24A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 63 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_24A.pep.xml -d "DECOY_" 4 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_24A.pep.xml 3 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_24A.pep.xml' 'interact-20161205_Sample_24A.prot.xml' 63 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_24A.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_24A.pep.xml' 4 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_24A.prot.xml' 0 sec job completed in 193 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_24.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_24.pep.xml' '20161205_Sample_24.pep.xml' -L'7'" file 1: 20161205_Sample_24.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_24.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_24.mzXML in msms_run_summary tag ... processed altogether 97662 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_24.pep.xml command completed in 42 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_24.pep.xml'" command completed in 1 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_24.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 12 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_24.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 49257 2+, 35590 3+, 8382 4+, 1874 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 27881 Decoys, and 67222 Non-Decoys Iterations: .........10.........20....... model complete after 28 iterations command completed in 64 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_24.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_24.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_24 (Comet)"... => Found 32024 hits. (0 decoys, 0 excluded) => Total so far: 32024 hits. (0 decoys, 0 excluded) command completed in 3 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_24.pep.xml" command completed in 3 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_24.pep.xml' 'interact-20161205_Sample_24.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_24.pep.xml... ...read in 0 1+, 18981 2+, 10899 3+, 1983 4+, 161 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 24798 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 8520 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 9652 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9652 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9652 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9652 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9652 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9652 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6275 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 9652 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=5.76465e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_24.prot.xml command completed in 60 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_24.prot.xml" Analyzing interact-20161205_Sample_24.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_24.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_24.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_24... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 11:03:36 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_24.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_24.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 11:03:40 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 4 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_24.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_24.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 11:03:40 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_24.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_24.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 11:03:40 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_24.pep.xml' '20161205_Sample_24.pep.xml' -L'7' 42 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_24.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_24.pep.xml' 'Cg-Giga_cont_AA.fa' 12 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_24.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 64 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_24.pep.xml -d "DECOY_" 3 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_24.pep.xml 3 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_24.pep.xml' 'interact-20161205_Sample_24.prot.xml' 60 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_24.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_24.pep.xml' 4 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_24.prot.xml' 0 sec job completed in 190 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_27A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_27A.pep.xml' '20161205_Sample_27A.pep.xml' -L'7'" file 1: 20161205_Sample_27A.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_27A.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_27A.mzXML in msms_run_summary tag ... processed altogether 96837 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_27A.pep.xml command completed in 43 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_27A.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_27A.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 12 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_27A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 51809 2+, 34018 3+, 7035 4+, 1634 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 29059 Decoys, and 65437 Non-Decoys Iterations: .........10.........20....... model complete after 28 iterations command completed in 62 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_27A.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_27A.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_27A (Comet)"... => Found 29418 hits. (0 decoys, 0 excluded) => Total so far: 29418 hits. (0 decoys, 0 excluded) command completed in 4 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_27A.pep.xml" command completed in 3 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_27A.pep.xml' 'interact-20161205_Sample_27A.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_27A.pep.xml... ...read in 0 1+, 17792 2+, 9779 3+, 1698 4+, 149 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 22967 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 8308 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 9428 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9428 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9428 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9428 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9428 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6047 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 9428 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=5.1794e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_27A.prot.xml command completed in 53 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_27A.prot.xml" Analyzing interact-20161205_Sample_27A.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_27A.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_27A.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_27A... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 11:06:38 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_27A.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_27A.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 11:06:42 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 4 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_27A.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_27A.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 11:06:42 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_27A.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_27A.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 11:06:42 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_27A.pep.xml' '20161205_Sample_27A.pep.xml' -L'7' 43 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_27A.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_27A.pep.xml' 'Cg-Giga_cont_AA.fa' 12 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_27A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 62 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_27A.pep.xml -d "DECOY_" 4 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_27A.pep.xml 3 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_27A.pep.xml' 'interact-20161205_Sample_27A.prot.xml' 53 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_27A.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_27A.pep.xml' 4 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_27A.prot.xml' 0 sec job completed in 182 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_27.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_27.pep.xml' '20161205_Sample_27.pep.xml' -L'7'" file 1: 20161205_Sample_27.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_27.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_27.mzXML in msms_run_summary tag ... processed altogether 97234 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_27.pep.xml command completed in 42 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_27.pep.xml'" command completed in 1 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_27.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 11 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_27.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 50325 2+, 34253 3+, 7983 4+, 1790 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 28716 Decoys, and 65635 Non-Decoys Iterations: .........10.........20....... model complete after 28 iterations command completed in 64 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_27.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_27.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_27 (Comet)"... => Found 29087 hits. (0 decoys, 0 excluded) => Total so far: 29087 hits. (0 decoys, 0 excluded) command completed in 3 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_27.pep.xml" command completed in 3 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_27.pep.xml' 'interact-20161205_Sample_27.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_27.pep.xml... ...read in 0 1+, 17245 2+, 9831 3+, 1852 4+, 159 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 22502 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 8410 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 9524 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9524 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9524 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9524 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9524 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9524 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6025 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 9524 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=5.53123e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_27.prot.xml command completed in 53 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_27.prot.xml" Analyzing interact-20161205_Sample_27.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_27.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_27.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_27... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 11:09:40 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_27.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_27.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 11:09:44 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 4 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_27.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_27.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 11:09:44 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_27.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_27.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 11:09:44 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_27.pep.xml' '20161205_Sample_27.pep.xml' -L'7' 42 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_27.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_27.pep.xml' 'Cg-Giga_cont_AA.fa' 11 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_27.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 64 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_27.pep.xml -d "DECOY_" 3 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_27.pep.xml 3 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_27.pep.xml' 'interact-20161205_Sample_27.prot.xml' 53 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_27.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_27.pep.xml' 4 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_27.prot.xml' 0 sec job completed in 182 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_28A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_28A.pep.xml' '20161205_Sample_28A.pep.xml' -L'7'" file 1: 20161205_Sample_28A.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_28A.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_28A.mzXML in msms_run_summary tag ... processed altogether 97504 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_28A.pep.xml command completed in 42 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_28A.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_28A.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 12 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_28A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 49043 2+, 36588 3+, 8050 4+, 1632 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 24853 Decoys, and 70460 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 62 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_28A.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_28A.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_28A (Comet)"... => Found 38326 hits. (0 decoys, 0 excluded) => Total so far: 38326 hits. (0 decoys, 0 excluded) command completed in 4 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_28A.pep.xml" command completed in 4 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_28A.pep.xml' 'interact-20161205_Sample_28A.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_28A.pep.xml... ...read in 0 1+, 22554 2+, 13088 3+, 2401 4+, 283 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 30065 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 9510 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10733 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10733 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10733 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10733 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10733 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10733 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 7019 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10733 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.53827e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_28A.prot.xml command completed in 74 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_28A.prot.xml" Analyzing interact-20161205_Sample_28A.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_28A.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_28A.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_28A... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 11:13:03 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_28A.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_28A.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 11:13:08 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_28A.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_28A.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 11:13:08 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_28A.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_28A.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 11:13:08 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_28A.pep.xml' '20161205_Sample_28A.pep.xml' -L'7' 42 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_28A.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_28A.pep.xml' 'Cg-Giga_cont_AA.fa' 12 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_28A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 62 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_28A.pep.xml -d "DECOY_" 4 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_28A.pep.xml 4 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_28A.pep.xml' 'interact-20161205_Sample_28A.prot.xml' 74 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_28A.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_28A.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_28A.prot.xml' 0 sec job completed in 204 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_28.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_28.pep.xml' '20161205_Sample_28.pep.xml' -L'7'" file 1: 20161205_Sample_28.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_28.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_28.mzXML in msms_run_summary tag ... processed altogether 96538 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_28.pep.xml command completed in 42 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_28.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_28.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 12 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_28.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 45950 2+, 37688 3+, 8780 4+, 1668 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 24120 Decoys, and 69966 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 61 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_28.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_28.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_28 (Comet)"... => Found 38767 hits. (0 decoys, 0 excluded) => Total so far: 38767 hits. (0 decoys, 0 excluded) command completed in 4 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_28.pep.xml" command completed in 4 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_28.pep.xml' 'interact-20161205_Sample_28.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_28.pep.xml... ...read in 0 1+, 21871 2+, 14179 3+, 2486 4+, 231 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 28468 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 9223 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10433 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10433 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10433 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10433 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10433 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10433 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10433 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6899 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10433 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.59475e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_28.prot.xml command completed in 75 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_28.prot.xml" Analyzing interact-20161205_Sample_28.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_28.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_28.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_28... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 11:16:27 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_28.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_28.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 11:16:32 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_28.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_28.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 11:16:32 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_28.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_28.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 11:16:32 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_28.pep.xml' '20161205_Sample_28.pep.xml' -L'7' 42 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_28.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_28.pep.xml' 'Cg-Giga_cont_AA.fa' 12 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_28.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 61 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_28.pep.xml -d "DECOY_" 4 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_28.pep.xml 4 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_28.pep.xml' 'interact-20161205_Sample_28.prot.xml' 75 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_28.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_28.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_28.prot.xml' 0 sec job completed in 204 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_32A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_32A.pep.xml' '20161205_Sample_32A.pep.xml' -L'7'" file 1: 20161205_Sample_32A.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_32A.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_32A.mzXML in msms_run_summary tag ... processed altogether 96330 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_32A.pep.xml command completed in 42 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_32A.pep.xml'" command completed in 1 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_32A.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 11 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_32A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 42588 2+, 38189 3+, 10676 4+, 2514 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 24823 Decoys, and 69144 Non-Decoys Iterations: .........10.........20....... model complete after 28 iterations command completed in 63 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_32A.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_32A.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_32A (Comet)"... => Found 36442 hits. (0 decoys, 0 excluded) => Total so far: 36442 hits. (0 decoys, 0 excluded) command completed in 4 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_32A.pep.xml" command completed in 4 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_32A.pep.xml' 'interact-20161205_Sample_32A.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_32A.pep.xml... ...read in 0 1+, 18882 2+, 13803 3+, 3299 4+, 458 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 28223 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 8903 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10051 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10051 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10051 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10051 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10051 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10051 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6497 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10051 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.67111e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_32A.prot.xml command completed in 73 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_32A.prot.xml" Analyzing interact-20161205_Sample_32A.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_32A.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_32A.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_32A... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 11:19:51 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_32A.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_32A.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 11:19:56 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_32A.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_32A.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 11:19:56 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_32A.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_32A.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 11:19:56 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_32A.pep.xml' '20161205_Sample_32A.pep.xml' -L'7' 42 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_32A.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_32A.pep.xml' 'Cg-Giga_cont_AA.fa' 11 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_32A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 63 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_32A.pep.xml -d "DECOY_" 4 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_32A.pep.xml 4 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_32A.pep.xml' 'interact-20161205_Sample_32A.prot.xml' 73 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_32A.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_32A.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_32A.prot.xml' 0 sec job completed in 204 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_32.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_32.pep.xml' '20161205_Sample_32.pep.xml' -L'7'" file 1: 20161205_Sample_32.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_32.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_32.mzXML in msms_run_summary tag ... processed altogether 96374 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_32.pep.xml command completed in 42 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_32.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_32.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 12 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_32.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 41072 2+, 38197 3+, 11287 4+, 3040 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 24764 Decoys, and 68832 Non-Decoys Iterations: .........10.........20....... model complete after 28 iterations command completed in 63 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_32.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_32.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_32 (Comet)"... => Found 36630 hits. (0 decoys, 0 excluded) => Total so far: 36630 hits. (0 decoys, 0 excluded) command completed in 4 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_32.pep.xml" command completed in 3 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_32.pep.xml' 'interact-20161205_Sample_32.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_32.pep.xml... ...read in 0 1+, 18804 2+, 13951 3+, 3406 4+, 469 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 28069 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 8923 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10086 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10086 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10086 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10086 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10086 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10086 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10086 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6577 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10086 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.69568e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_32.prot.xml command completed in 75 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_32.prot.xml" Analyzing interact-20161205_Sample_32.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_32.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_32.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_32... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 11:23:16 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_32.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_32.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 11:23:21 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_32.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_32.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 11:23:21 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_32.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_32.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 11:23:21 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_32.pep.xml' '20161205_Sample_32.pep.xml' -L'7' 42 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_32.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_32.pep.xml' 'Cg-Giga_cont_AA.fa' 12 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_32.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 63 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_32.pep.xml -d "DECOY_" 4 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_32.pep.xml 3 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_32.pep.xml' 'interact-20161205_Sample_32.prot.xml' 75 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_32.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_32.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_32.prot.xml' 0 sec job completed in 205 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_35A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_35A.pep.xml' '20161205_Sample_35A.pep.xml' -L'7'" file 1: 20161205_Sample_35A.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_35A.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_35A.mzXML in msms_run_summary tag ... processed altogether 84905 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_35A.pep.xml command completed in 38 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_35A.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_35A.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 10 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_35A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 50986 2+, 23934 3+, 5657 4+, 1532 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 31793 Decoys, and 50316 Non-Decoys Iterations: .........10.........20......... model complete after 30 iterations command completed in 57 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_35A.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_35A.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_35A (Comet)"... => Found 11775 hits. (0 decoys, 0 excluded) => Total so far: 11775 hits. (0 decoys, 0 excluded) command completed in 2 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_35A.pep.xml" command completed in 1 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_35A.pep.xml' 'interact-20161205_Sample_35A.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_35A.pep.xml... ...read in 0 1+, 7335 2+, 3774 3+, 622 4+, 44 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 9506 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 5511 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 6335 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 6335 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 6335 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 6335 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 6335 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 6335 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 3754 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 6335 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=3.02076e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_35A.prot.xml command completed in 19 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_35A.prot.xml" Analyzing interact-20161205_Sample_35A.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_35A.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_35A.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_35A... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 11:25:29 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_35A.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_35A.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 11:25:30 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_35A.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_35A.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 11:25:30 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_35A.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_35A.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 11:25:30 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_35A.pep.xml' '20161205_Sample_35A.pep.xml' -L'7' 38 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_35A.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_35A.pep.xml' 'Cg-Giga_cont_AA.fa' 10 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_35A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 57 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_35A.pep.xml -d "DECOY_" 2 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_35A.pep.xml 1 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_35A.pep.xml' 'interact-20161205_Sample_35A.prot.xml' 19 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_35A.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_35A.pep.xml' 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_35A.prot.xml' 0 sec job completed in 129 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_35.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_35.pep.xml' '20161205_Sample_35.pep.xml' -L'7'" file 1: 20161205_Sample_35.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_35.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_35.mzXML in msms_run_summary tag ... processed altogether 86040 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_35.pep.xml command completed in 38 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_35.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_35.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 11 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_35.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 51121 2+, 24514 3+, 5904 4+, 1529 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 32318 Decoys, and 50750 Non-Decoys Iterations: .........10.........20........ model complete after 29 iterations command completed in 56 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_35.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_35.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_35 (Comet)"... => Found 12085 hits. (0 decoys, 0 excluded) => Total so far: 12085 hits. (0 decoys, 0 excluded) command completed in 1 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_35.pep.xml" command completed in 2 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_35.pep.xml' 'interact-20161205_Sample_35.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_35.pep.xml... ...read in 0 1+, 7521 2+, 3861 3+, 659 4+, 44 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 9682 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 5532 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 6370 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 6370 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 6370 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 6370 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 6370 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 3832 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 6370 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=2.9665e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_35.prot.xml command completed in 19 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_35.prot.xml" Analyzing interact-20161205_Sample_35.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_35.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_35.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_35... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 11:27:38 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_35.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_35.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 11:27:39 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_35.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_35.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 11:27:39 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_35.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_35.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 11:27:39 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_35.pep.xml' '20161205_Sample_35.pep.xml' -L'7' 38 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_35.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_35.pep.xml' 'Cg-Giga_cont_AA.fa' 11 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_35.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 56 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_35.pep.xml -d "DECOY_" 1 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_35.pep.xml 2 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_35.pep.xml' 'interact-20161205_Sample_35.prot.xml' 19 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_35.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_35.pep.xml' 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_35.prot.xml' 0 sec job completed in 129 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_36A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_36A.pep.xml' '20161205_Sample_36A.pep.xml' -L'7'" file 1: 20161205_Sample_36A.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_36A.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_36A.mzXML in msms_run_summary tag ... processed altogether 95308 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_36A.pep.xml command completed in 42 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_36A.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_36A.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 12 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_36A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 40309 2+, 38578 3+, 11250 4+, 2614 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 24958 Decoys, and 67793 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 60 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_36A.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_36A.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_36A (Comet)"... => Found 34901 hits. (0 decoys, 0 excluded) => Total so far: 34901 hits. (0 decoys, 0 excluded) command completed in 4 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_36A.pep.xml" command completed in 4 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_36A.pep.xml' 'interact-20161205_Sample_36A.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_36A.pep.xml... ...read in 0 1+, 17379 2+, 13691 3+, 3375 4+, 456 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 27008 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 8658 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 9803 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9803 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9803 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9803 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9803 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9803 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6378 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 9803 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.41576e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_36A.prot.xml command completed in 67 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_36A.prot.xml" Analyzing interact-20161205_Sample_36A.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_36A.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_36A.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_36A... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 11:30:49 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_36A.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_36A.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 11:30:54 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_36A.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_36A.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 11:30:54 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_36A.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_36A.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 11:30:54 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_36A.pep.xml' '20161205_Sample_36A.pep.xml' -L'7' 42 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_36A.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_36A.pep.xml' 'Cg-Giga_cont_AA.fa' 12 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_36A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 60 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_36A.pep.xml -d "DECOY_" 4 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_36A.pep.xml 4 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_36A.pep.xml' 'interact-20161205_Sample_36A.prot.xml' 67 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_36A.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_36A.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_36A.prot.xml' 0 sec job completed in 195 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_36.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_36.pep.xml' '20161205_Sample_36.pep.xml' -L'7'" file 1: 20161205_Sample_36.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_36.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_36.mzXML in msms_run_summary tag ... processed altogether 96434 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_36.pep.xml command completed in 42 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_36.pep.xml'" command completed in 1 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_36.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 11 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_36.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 41369 2+, 38063 3+, 11529 4+, 2865 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 24763 Decoys, and 69063 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 61 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_36.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_36.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_36 (Comet)"... => Found 36046 hits. (0 decoys, 0 excluded) => Total so far: 36046 hits. (0 decoys, 0 excluded) command completed in 4 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_36.pep.xml" command completed in 4 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_36.pep.xml' 'interact-20161205_Sample_36.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_36.pep.xml... ...read in 0 1+, 18447 2+, 13729 3+, 3409 4+, 461 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 27181 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 8978 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10162 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10162 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10162 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10162 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10162 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10162 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6555 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10162 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.5868e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_36.prot.xml command completed in 71 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_36.prot.xml" Analyzing interact-20161205_Sample_36.prot.xml ... command completed in 0 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_36.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_36.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_36... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 11:34:08 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_36.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_36.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 11:34:13 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_36.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_36.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 11:34:13 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_36.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_36.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 11:34:13 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_36.pep.xml' '20161205_Sample_36.pep.xml' -L'7' 42 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_36.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_36.pep.xml' 'Cg-Giga_cont_AA.fa' 11 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_36.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 61 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_36.pep.xml -d "DECOY_" 4 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_36.pep.xml 4 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_36.pep.xml' 'interact-20161205_Sample_36.prot.xml' 71 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_36.prot.xml 0 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_36.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_36.prot.xml' 0 sec job completed in 199 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_3A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_3A.pep.xml' '20161205_Sample_3A.pep.xml' -L'7'" file 1: 20161205_Sample_3A.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_3A.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_3A.mzXML in msms_run_summary tag ... processed altogether 90755 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_3A.pep.xml command completed in 40 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_3A.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_3A.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 11 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_3A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 40414 2+, 36656 3+, 9303 4+, 2006 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 22176 Decoys, and 66203 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 58 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_3A.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_3A.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_3A (Comet)"... => Found 36750 hits. (0 decoys, 0 excluded) => Total so far: 36750 hits. (0 decoys, 0 excluded) command completed in 4 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_3A.pep.xml" command completed in 3 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_3A.pep.xml' 'interact-20161205_Sample_3A.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_3A.pep.xml... ...read in 0 1+, 19285 2+, 14315 3+, 2811 4+, 339 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 28600 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 9274 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10465 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10465 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10465 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10465 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10465 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10465 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6871 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10465 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.18979e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_3A.prot.xml command completed in 74 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_3A.prot.xml" Analyzing interact-20161205_Sample_3A.prot.xml ... command completed in 0 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_3A.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_3A.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_3A... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 11:37:24 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_3A.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_3A.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 11:37:28 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_3A.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_3A.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 11:37:29 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_3A.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_3A.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 11:37:29 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 1 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_3A.pep.xml' '20161205_Sample_3A.pep.xml' -L'7' 40 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_3A.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_3A.pep.xml' 'Cg-Giga_cont_AA.fa' 11 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_3A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 58 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_3A.pep.xml -d "DECOY_" 4 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_3A.pep.xml 3 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_3A.pep.xml' 'interact-20161205_Sample_3A.prot.xml' 74 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_3A.prot.xml 0 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_3A.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_3A.prot.xml' 1 sec job completed in 196 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_3.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_3.pep.xml' '20161205_Sample_3.pep.xml' -L'7'" file 1: 20161205_Sample_3.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_3.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_3.mzXML in msms_run_summary tag ... processed altogether 90652 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_3.pep.xml command completed in 39 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_3.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_3.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 11 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_3.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 40560 2+, 36652 3+, 9207 4+, 1759 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 21962 Decoys, and 66216 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 57 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_3.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_3.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_3 (Comet)"... => Found 37017 hits. (0 decoys, 0 excluded) => Total so far: 37017 hits. (0 decoys, 0 excluded) command completed in 5 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_3.pep.xml" command completed in 3 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_3.pep.xml' 'interact-20161205_Sample_3.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_3.pep.xml... ...read in 0 1+, 19824 2+, 14236 3+, 2678 4+, 279 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 28869 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 9640 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10878 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10878 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10878 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10878 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10878 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10878 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10878 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 7043 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10878 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.4301e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_3.prot.xml command completed in 77 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_3.prot.xml" Analyzing interact-20161205_Sample_3.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_3.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_3.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_3... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 11:40:42 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_3.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_3.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 11:40:47 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_3.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_3.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 11:40:47 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_3.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_3.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 11:40:47 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_3.pep.xml' '20161205_Sample_3.pep.xml' -L'7' 39 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_3.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_3.pep.xml' 'Cg-Giga_cont_AA.fa' 11 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_3.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 57 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_3.pep.xml -d "DECOY_" 5 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_3.pep.xml 3 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_3.pep.xml' 'interact-20161205_Sample_3.prot.xml' 77 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_3.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_3.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_3.prot.xml' 0 sec job completed in 198 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_40A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_40A.pep.xml' '20161205_Sample_40A.pep.xml' -L'7'" file 1: 20161205_Sample_40A.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_40A.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_40A.mzXML in msms_run_summary tag ... processed altogether 92582 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_40A.pep.xml command completed in 41 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_40A.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_40A.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 11 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_40A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 37791 2+, 38172 3+, 11392 4+, 2885 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 24079 Decoys, and 66161 Non-Decoys Iterations: .........10.........20....... model complete after 28 iterations command completed in 61 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_40A.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_40A.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_40A (Comet)"... => Found 34538 hits. (0 decoys, 0 excluded) => Total so far: 34538 hits. (0 decoys, 0 excluded) command completed in 3 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_40A.pep.xml" command completed in 4 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_40A.pep.xml' 'interact-20161205_Sample_40A.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_40A.pep.xml... ...read in 0 1+, 16866 2+, 13806 3+, 3371 4+, 495 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 26672 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 8654 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 9788 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9788 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9788 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9788 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9788 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9788 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6376 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 9788 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.43797e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_40A.prot.xml command completed in 69 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_40A.prot.xml" Analyzing interact-20161205_Sample_40A.prot.xml ... command completed in 0 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_40A.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_40A.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_40A... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 11:43:56 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_40A.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_40A.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 11:44:01 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_40A.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_40A.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 11:44:01 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_40A.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_40A.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 11:44:01 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_40A.pep.xml' '20161205_Sample_40A.pep.xml' -L'7' 41 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_40A.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_40A.pep.xml' 'Cg-Giga_cont_AA.fa' 11 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_40A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 61 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_40A.pep.xml -d "DECOY_" 3 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_40A.pep.xml 4 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_40A.pep.xml' 'interact-20161205_Sample_40A.prot.xml' 69 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_40A.prot.xml 0 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_40A.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_40A.prot.xml' 0 sec job completed in 194 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_40.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_40.pep.xml' '20161205_Sample_40.pep.xml' -L'7'" file 1: 20161205_Sample_40.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_40.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_40.mzXML in msms_run_summary tag ... processed altogether 91598 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_40.pep.xml command completed in 40 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_40.pep.xml'" command completed in 1 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_40.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 11 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_40.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 37077 2+, 37293 3+, 11576 4+, 2977 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 23130 Decoys, and 65793 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 58 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_40.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_40.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_40 (Comet)"... => Found 35211 hits. (0 decoys, 0 excluded) => Total so far: 35211 hits. (0 decoys, 0 excluded) command completed in 4 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_40.pep.xml" command completed in 3 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_40.pep.xml' 'interact-20161205_Sample_40.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_40.pep.xml... ...read in 0 1+, 17269 2+, 14012 3+, 3458 4+, 472 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 26577 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 8806 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 9967 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9967 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9967 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9967 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9967 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9967 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6431 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 9967 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.44684e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_40.prot.xml command completed in 70 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_40.prot.xml" Analyzing interact-20161205_Sample_40.prot.xml ... command completed in 0 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_40.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_40.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_40... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 11:47:08 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_40.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_40.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 11:47:13 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_40.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_40.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 11:47:13 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_40.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_40.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 11:47:13 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_40.pep.xml' '20161205_Sample_40.pep.xml' -L'7' 40 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_40.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_40.pep.xml' 'Cg-Giga_cont_AA.fa' 11 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_40.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 58 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_40.pep.xml -d "DECOY_" 4 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_40.pep.xml 3 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_40.pep.xml' 'interact-20161205_Sample_40.prot.xml' 70 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_40.prot.xml 0 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_40.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_40.prot.xml' 0 sec job completed in 192 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_43A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_43A.pep.xml' '20161205_Sample_43A.pep.xml' -L'7'" file 1: 20161205_Sample_43A.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_43A.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_43A.mzXML in msms_run_summary tag ... processed altogether 88214 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_43A.pep.xml command completed in 39 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_43A.pep.xml'" command completed in 1 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_43A.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 10 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_43A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 54763 2+, 24387 3+, 5164 4+, 1568 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 31273 Decoys, and 54609 Non-Decoys Iterations: .........10.........20....... model complete after 28 iterations command completed in 57 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_43A.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_43A.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_43A (Comet)"... => Found 17061 hits. (0 decoys, 0 excluded) => Total so far: 17061 hits. (0 decoys, 0 excluded) command completed in 2 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_43A.pep.xml" command completed in 2 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_43A.pep.xml' 'interact-20161205_Sample_43A.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_43A.pep.xml... ...read in 0 1+, 11378 2+, 4970 3+, 652 4+, 61 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 13647 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 6626 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 7561 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 7561 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 7561 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 7561 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 7561 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 4631 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 7561 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=3.87219e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_43A.prot.xml command completed in 28 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_43A.prot.xml" Analyzing interact-20161205_Sample_43A.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_43A.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_43A.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_43A... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 11:49:33 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_43A.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_43A.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 11:49:35 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 2 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_43A.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_43A.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 11:49:35 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_43A.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_43A.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 11:49:35 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_43A.pep.xml' '20161205_Sample_43A.pep.xml' -L'7' 39 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_43A.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_43A.pep.xml' 'Cg-Giga_cont_AA.fa' 10 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_43A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 57 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_43A.pep.xml -d "DECOY_" 2 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_43A.pep.xml 2 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_43A.pep.xml' 'interact-20161205_Sample_43A.prot.xml' 28 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_43A.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_43A.pep.xml' 2 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_43A.prot.xml' 0 sec job completed in 142 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_43.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_43.pep.xml' '20161205_Sample_43.pep.xml' -L'7'" file 1: 20161205_Sample_43.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_43.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_43.mzXML in msms_run_summary tag ... processed altogether 89306 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_43.pep.xml command completed in 40 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_43.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_43.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 11 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_43.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 53897 2+, 25238 3+, 5735 4+, 1609 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 31763 Decoys, and 54716 Non-Decoys Iterations: .........10.........20........ model complete after 29 iterations command completed in 59 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_43.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_43.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_43 (Comet)"... => Found 16916 hits. (0 decoys, 0 excluded) => Total so far: 16916 hits. (0 decoys, 0 excluded) command completed in 2 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_43.pep.xml" command completed in 2 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_43.pep.xml' 'interact-20161205_Sample_43.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_43.pep.xml... ...read in 0 1+, 11128 2+, 5058 3+, 689 4+, 41 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 13526 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 6697 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 7634 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 7634 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 7634 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 7634 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 7634 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 7634 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 4670 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 7634 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=3.85772e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_43.prot.xml command completed in 28 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_43.prot.xml" Analyzing interact-20161205_Sample_43.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_43.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_43.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_43... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 11:51:58 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_43.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_43.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 11:52:00 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 2 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_43.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_43.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 11:52:00 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_43.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_43.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 11:52:00 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_43.pep.xml' '20161205_Sample_43.pep.xml' -L'7' 40 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_43.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_43.pep.xml' 'Cg-Giga_cont_AA.fa' 11 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_43.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 59 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_43.pep.xml -d "DECOY_" 2 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_43.pep.xml 2 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_43.pep.xml' 'interact-20161205_Sample_43.prot.xml' 28 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_43.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_43.pep.xml' 2 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_43.prot.xml' 0 sec job completed in 145 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_44A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_44A.pep.xml' '20161205_Sample_44A.pep.xml' -L'7'" file 1: 20161205_Sample_44A.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_44A.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_44A.mzXML in msms_run_summary tag ... processed altogether 93883 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_44A.pep.xml command completed in 41 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_44A.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_44A.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 12 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_44A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 49592 2+, 33069 3+, 6949 4+, 1762 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 26992 Decoys, and 64380 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 59 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_44A.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_44A.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_44A (Comet)"... => Found 29787 hits. (0 decoys, 0 excluded) => Total so far: 29787 hits. (0 decoys, 0 excluded) command completed in 3 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_44A.pep.xml" command completed in 3 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_44A.pep.xml' 'interact-20161205_Sample_44A.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_44A.pep.xml... ...read in 0 1+, 17794 2+, 10032 3+, 1767 4+, 194 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 23431 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 8667 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 9826 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9826 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9826 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9826 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9826 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6170 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 9826 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=5.49088e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_44A.prot.xml command completed in 57 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_44A.prot.xml" Analyzing interact-20161205_Sample_44A.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_44A.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_44A.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_44A... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 11:54:56 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_44A.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_44A.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 11:55:00 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 4 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_44A.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_44A.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 11:55:00 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_44A.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_44A.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 11:55:00 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_44A.pep.xml' '20161205_Sample_44A.pep.xml' -L'7' 41 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_44A.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_44A.pep.xml' 'Cg-Giga_cont_AA.fa' 12 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_44A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 59 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_44A.pep.xml -d "DECOY_" 3 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_44A.pep.xml 3 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_44A.pep.xml' 'interact-20161205_Sample_44A.prot.xml' 57 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_44A.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_44A.pep.xml' 4 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_44A.prot.xml' 0 sec job completed in 180 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_44.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_44.pep.xml' '20161205_Sample_44.pep.xml' -L'7'" file 1: 20161205_Sample_44.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_44.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_44.mzXML in msms_run_summary tag ... processed altogether 93502 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_44.pep.xml command completed in 41 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_44.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_44.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 12 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_44.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 47695 2+, 33399 3+, 7736 4+, 1993 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 26775 Decoys, and 64048 Non-Decoys Iterations: .........10.........20....... model complete after 28 iterations command completed in 60 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_44.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_44.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_44 (Comet)"... => Found 29529 hits. (0 decoys, 0 excluded) => Total so far: 29529 hits. (0 decoys, 0 excluded) command completed in 4 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_44.pep.xml" command completed in 3 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_44.pep.xml' 'interact-20161205_Sample_44.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_44.pep.xml... ...read in 0 1+, 17054 2+, 10374 3+, 1887 4+, 214 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 22936 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 8270 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 9380 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9380 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9380 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9380 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9380 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6007 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 9380 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=5.4995e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_44.prot.xml command completed in 55 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_44.prot.xml" Analyzing interact-20161205_Sample_44.prot.xml ... command completed in 0 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_44.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_44.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_44... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 11:57:55 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_44.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_44.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 11:57:59 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 4 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_44.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_44.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 11:57:59 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_44.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_44.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 11:57:59 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_44.pep.xml' '20161205_Sample_44.pep.xml' -L'7' 41 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_44.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_44.pep.xml' 'Cg-Giga_cont_AA.fa' 12 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_44.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 60 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_44.pep.xml -d "DECOY_" 4 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_44.pep.xml 3 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_44.pep.xml' 'interact-20161205_Sample_44.prot.xml' 55 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_44.prot.xml 0 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_44.pep.xml' 4 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_44.prot.xml' 0 sec job completed in 179 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_48A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_48A.pep.xml' '20161205_Sample_48A.pep.xml' -L'7'" file 1: 20161205_Sample_48A.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_48A.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_48A.mzXML in msms_run_summary tag ... processed altogether 100181 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_48A.pep.xml command completed in 43 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_48A.pep.xml'" command completed in 1 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_48A.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 11 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_48A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 50416 2+, 37052 3+, 8393 4+, 1951 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 24774 Decoys, and 73038 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 65 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_48A.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_48A.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_48A (Comet)"... => Found 40472 hits. (0 decoys, 0 excluded) => Total so far: 40472 hits. (0 decoys, 0 excluded) command completed in 4 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_48A.pep.xml" command completed in 4 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_48A.pep.xml' 'interact-20161205_Sample_48A.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_48A.pep.xml... ...read in 0 1+, 23782 2+, 13772 3+, 2588 4+, 330 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 30794 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 9658 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10947 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10947 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10947 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10947 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10947 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10947 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 7097 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10947 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.60396e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_48A.prot.xml command completed in 86 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_48A.prot.xml" Analyzing interact-20161205_Sample_48A.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_48A.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_48A.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_48A... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 12:01:34 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_48A.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_48A.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 12:01:39 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_48A.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_48A.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 12:01:40 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_48A.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_48A.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 12:01:40 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 1 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_48A.pep.xml' '20161205_Sample_48A.pep.xml' -L'7' 43 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_48A.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_48A.pep.xml' 'Cg-Giga_cont_AA.fa' 11 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_48A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 65 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_48A.pep.xml -d "DECOY_" 4 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_48A.pep.xml 4 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_48A.pep.xml' 'interact-20161205_Sample_48A.prot.xml' 86 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_48A.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_48A.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_48A.prot.xml' 1 sec job completed in 221 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_48.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_48.pep.xml' '20161205_Sample_48.pep.xml' -L'7'" file 1: 20161205_Sample_48.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_48.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_48.mzXML in msms_run_summary tag ... processed altogether 97644 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_48.pep.xml command completed in 42 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_48.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_48.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 12 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_48.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 45652 2+, 37607 3+, 9291 4+, 2493 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 24124 Decoys, and 70919 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 62 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_48.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_48.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_48 (Comet)"... => Found 39279 hits. (0 decoys, 0 excluded) => Total so far: 39279 hits. (0 decoys, 0 excluded) command completed in 5 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_48.pep.xml" command completed in 4 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_48.pep.xml' 'interact-20161205_Sample_48.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_48.pep.xml... ...read in 0 1+, 21809 2+, 14241 3+, 2863 4+, 366 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 29381 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 9418 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10635 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10635 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10635 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10635 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10635 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10635 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6939 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10635 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.58989e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_48.prot.xml command completed in 76 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_48.prot.xml" Analyzing interact-20161205_Sample_48.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_48.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_48.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_48... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 12:05:02 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_48.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_48.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 12:05:07 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_48.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_48.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 12:05:07 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_48.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_48.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 12:05:07 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_48.pep.xml' '20161205_Sample_48.pep.xml' -L'7' 42 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_48.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_48.pep.xml' 'Cg-Giga_cont_AA.fa' 12 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_48.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 62 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_48.pep.xml -d "DECOY_" 5 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_48.pep.xml 4 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_48.pep.xml' 'interact-20161205_Sample_48.prot.xml' 76 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_48.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_48.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_48.prot.xml' 0 sec job completed in 207 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_4A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_4A.pep.xml' '20161205_Sample_4A.pep.xml' -L'7'" file 1: 20161205_Sample_4A.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_4A.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_4A.mzXML in msms_run_summary tag ... processed altogether 94919 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_4A.pep.xml command completed in 42 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_4A.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_4A.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 12 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_4A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 43668 2+, 37971 3+, 9039 4+, 2029 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 22749 Decoys, and 69958 Non-Decoys Iterations: .........10.........20....... model complete after 28 iterations command completed in 62 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_4A.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_4A.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_4A (Comet)"... => Found 40007 hits. (0 decoys, 0 excluded) => Total so far: 40007 hits. (0 decoys, 0 excluded) command completed in 5 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_4A.pep.xml" command completed in 4 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_4A.pep.xml' 'interact-20161205_Sample_4A.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_4A.pep.xml... ...read in 0 1+, 21885 2+, 14945 3+, 2830 4+, 347 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 30484 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 9681 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10913 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10913 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10913 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10913 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10913 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10913 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10913 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10913 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 7133 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10913 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.76596e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_4A.prot.xml command completed in 80 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_4A.prot.xml" Analyzing interact-20161205_Sample_4A.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_4A.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_4A.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_4A... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 12:08:33 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_4A.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_4A.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 12:08:38 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_4A.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_4A.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 12:08:38 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_4A.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_4A.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 12:08:38 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_4A.pep.xml' '20161205_Sample_4A.pep.xml' -L'7' 42 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_4A.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_4A.pep.xml' 'Cg-Giga_cont_AA.fa' 12 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_4A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 62 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_4A.pep.xml -d "DECOY_" 5 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_4A.pep.xml 4 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_4A.pep.xml' 'interact-20161205_Sample_4A.prot.xml' 80 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_4A.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_4A.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_4A.prot.xml' 0 sec job completed in 211 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_4.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_4.pep.xml' '20161205_Sample_4.pep.xml' -L'7'" file 1: 20161205_Sample_4.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_4.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_4.mzXML in msms_run_summary tag ... processed altogether 93878 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_4.pep.xml command completed in 42 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_4.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_4.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 11 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_4.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 42206 2+, 37669 3+, 9587 4+, 1957 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 22248 Decoys, and 69171 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 60 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_4.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_4.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_4 (Comet)"... => Found 40177 hits. (0 decoys, 0 excluded) => Total so far: 40177 hits. (0 decoys, 0 excluded) command completed in 5 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_4.pep.xml" command completed in 4 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_4.pep.xml' 'interact-20161205_Sample_4.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_4.pep.xml... ...read in 0 1+, 21522 2+, 15321 3+, 3039 4+, 295 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 30326 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 9806 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 11110 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 11110 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 11110 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 11110 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 11110 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 7154 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 11110 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.66618e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_4.prot.xml command completed in 81 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_4.prot.xml" Analyzing interact-20161205_Sample_4.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_4.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_4.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_4... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 12:12:02 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_4.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_4.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 12:12:07 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_4.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_4.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 12:12:07 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_4.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_4.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 12:12:07 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_4.pep.xml' '20161205_Sample_4.pep.xml' -L'7' 42 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_4.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_4.pep.xml' 'Cg-Giga_cont_AA.fa' 11 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_4.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 60 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_4.pep.xml -d "DECOY_" 5 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_4.pep.xml 4 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_4.pep.xml' 'interact-20161205_Sample_4.prot.xml' 81 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_4.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_4.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_4.prot.xml' 0 sec job completed in 209 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_51A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_51A.pep.xml' '20161205_Sample_51A.pep.xml' -L'7'" file 1: 20161205_Sample_51A.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_51A.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_51A.mzXML in msms_run_summary tag ... processed altogether 92551 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_51A.pep.xml command completed in 41 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_51A.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_51A.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 12 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_51A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 46433 2+, 33782 3+, 7885 4+, 1946 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 25868 Decoys, and 64178 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 58 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_51A.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_51A.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_51A (Comet)"... => Found 30941 hits. (0 decoys, 0 excluded) => Total so far: 30941 hits. (0 decoys, 0 excluded) command completed in 3 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_51A.pep.xml" command completed in 3 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_51A.pep.xml' 'interact-20161205_Sample_51A.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_51A.pep.xml... ...read in 0 1+, 17918 2+, 10810 3+, 1999 4+, 214 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 24311 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 8693 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 9800 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9800 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9800 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9800 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9800 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9800 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6297 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 9800 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=5.66329e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_51A.prot.xml command completed in 57 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_51A.prot.xml" Analyzing interact-20161205_Sample_51A.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_51A.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_51A.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_51A... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 12:15:02 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_51A.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_51A.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 12:15:06 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 4 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_51A.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_51A.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 12:15:06 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_51A.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_51A.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 12:15:06 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_51A.pep.xml' '20161205_Sample_51A.pep.xml' -L'7' 41 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_51A.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_51A.pep.xml' 'Cg-Giga_cont_AA.fa' 12 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_51A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 58 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_51A.pep.xml -d "DECOY_" 3 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_51A.pep.xml 3 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_51A.pep.xml' 'interact-20161205_Sample_51A.prot.xml' 57 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_51A.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_51A.pep.xml' 4 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_51A.prot.xml' 0 sec job completed in 179 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_51.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_51.pep.xml' '20161205_Sample_51.pep.xml' -L'7'" file 1: 20161205_Sample_51.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_51.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_51.mzXML in msms_run_summary tag ... processed altogether 91634 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_51.pep.xml command completed in 40 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_51.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_51.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 12 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_51.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 44953 2+, 33385 3+, 8505 4+, 2016 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 25421 Decoys, and 63438 Non-Decoys Iterations: .........10.........20....... model complete after 28 iterations command completed in 59 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_51.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_51.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_51 (Comet)"... => Found 30941 hits. (0 decoys, 0 excluded) => Total so far: 30941 hits. (0 decoys, 0 excluded) command completed in 4 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_51.pep.xml" command completed in 3 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_51.pep.xml' 'interact-20161205_Sample_51.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_51.pep.xml... ...read in 0 1+, 17465 2+, 11195 3+, 2086 4+, 195 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 24253 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 8797 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 9963 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9963 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9963 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9963 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9963 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9963 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9963 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6337 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 9963 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=5.936e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_51.prot.xml command completed in 62 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_51.prot.xml" Analyzing interact-20161205_Sample_51.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_51.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_51.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_51... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 12:18:07 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_51.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_51.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 12:18:11 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 4 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_51.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_51.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 12:18:11 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_51.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_51.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 12:18:11 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_51.pep.xml' '20161205_Sample_51.pep.xml' -L'7' 40 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_51.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_51.pep.xml' 'Cg-Giga_cont_AA.fa' 12 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_51.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 59 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_51.pep.xml -d "DECOY_" 4 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_51.pep.xml 3 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_51.pep.xml' 'interact-20161205_Sample_51.prot.xml' 62 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_51.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_51.pep.xml' 4 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_51.prot.xml' 0 sec job completed in 185 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_52A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_52A.pep.xml' '20161205_Sample_52A.pep.xml' -L'7'" file 1: 20161205_Sample_52A.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_52A.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_52A.mzXML in msms_run_summary tag ... processed altogether 96309 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_52A.pep.xml command completed in 43 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_52A.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_52A.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 11 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_52A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 49269 2+, 34959 3+, 7592 4+, 2119 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 27015 Decoys, and 66924 Non-Decoys Iterations: .........10.........20....... model complete after 28 iterations command completed in 63 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_52A.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_52A.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_52A (Comet)"... => Found 32539 hits. (0 decoys, 0 excluded) => Total so far: 32539 hits. (0 decoys, 0 excluded) command completed in 4 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_52A.pep.xml" command completed in 3 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_52A.pep.xml' 'interact-20161205_Sample_52A.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_52A.pep.xml... ...read in 0 1+, 19012 2+, 11285 3+, 2012 4+, 230 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 25028 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 8942 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10093 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10093 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10093 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10093 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10093 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10093 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10093 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6411 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10093 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=5.65196e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_52A.prot.xml command completed in 64 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_52A.prot.xml" Analyzing interact-20161205_Sample_52A.prot.xml ... command completed in 0 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_52A.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_52A.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_52A... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 12:21:20 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_52A.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_52A.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 12:21:24 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_52A.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_52A.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 12:21:24 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_52A.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_52A.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 12:21:24 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_52A.pep.xml' '20161205_Sample_52A.pep.xml' -L'7' 43 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_52A.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_52A.pep.xml' 'Cg-Giga_cont_AA.fa' 11 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_52A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 63 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_52A.pep.xml -d "DECOY_" 4 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_52A.pep.xml 3 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_52A.pep.xml' 'interact-20161205_Sample_52A.prot.xml' 64 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_52A.prot.xml 0 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_52A.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_52A.prot.xml' 0 sec job completed in 193 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_52.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_52.pep.xml' '20161205_Sample_52.pep.xml' -L'7'" file 1: 20161205_Sample_52.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_52.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_52.mzXML in msms_run_summary tag ... processed altogether 95741 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_52.pep.xml command completed in 43 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_52.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_52.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 11 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_52.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 48780 2+, 33467 3+, 8442 4+, 2188 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 26140 Decoys, and 66737 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 61 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_52.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_52.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_52 (Comet)"... => Found 32999 hits. (0 decoys, 0 excluded) => Total so far: 32999 hits. (0 decoys, 0 excluded) command completed in 3 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_52.pep.xml" command completed in 4 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_52.pep.xml' 'interact-20161205_Sample_52.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_52.pep.xml... ...read in 0 1+, 19669 2+, 10933 3+, 2201 4+, 196 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 25138 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 9114 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10307 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10307 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10307 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10307 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10307 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6490 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10307 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.36643e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_52.prot.xml command completed in 61 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_52.prot.xml" Analyzing interact-20161205_Sample_52.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_52.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_52.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_52... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 12:24:28 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_52.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_52.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 12:24:33 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_52.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_52.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 12:24:33 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_52.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_52.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 12:24:33 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_52.pep.xml' '20161205_Sample_52.pep.xml' -L'7' 43 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_52.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_52.pep.xml' 'Cg-Giga_cont_AA.fa' 11 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_52.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 61 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_52.pep.xml -d "DECOY_" 3 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_52.pep.xml 4 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_52.pep.xml' 'interact-20161205_Sample_52.prot.xml' 61 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_52.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_52.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_52.prot.xml' 0 sec job completed in 189 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_56A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_56A.pep.xml' '20161205_Sample_56A.pep.xml' -L'7'" file 1: 20161205_Sample_56A.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_56A.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_56A.mzXML in msms_run_summary tag ... processed altogether 99158 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_56A.pep.xml command completed in 43 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_56A.pep.xml'" command completed in 1 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_56A.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 12 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_56A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 46129 2+, 38164 3+, 9897 4+, 2412 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 25632 Decoys, and 70970 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 63 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_56A.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_56A.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_56A (Comet)"... => Found 36852 hits. (0 decoys, 0 excluded) => Total so far: 36852 hits. (0 decoys, 0 excluded) command completed in 4 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_56A.pep.xml" command completed in 4 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_56A.pep.xml' 'interact-20161205_Sample_56A.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_56A.pep.xml... ...read in 0 1+, 20081 2+, 13357 3+, 3028 4+, 386 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 28147 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 8987 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10185 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10185 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10185 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10185 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10185 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6530 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10185 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.60896e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_56A.prot.xml command completed in 74 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_56A.prot.xml" Analyzing interact-20161205_Sample_56A.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_56A.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_56A.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_56A... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 12:27:55 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_56A.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_56A.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 12:28:00 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_56A.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_56A.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 12:28:00 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_56A.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_56A.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 12:28:00 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_56A.pep.xml' '20161205_Sample_56A.pep.xml' -L'7' 43 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_56A.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_56A.pep.xml' 'Cg-Giga_cont_AA.fa' 12 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_56A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 63 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_56A.pep.xml -d "DECOY_" 4 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_56A.pep.xml 4 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_56A.pep.xml' 'interact-20161205_Sample_56A.prot.xml' 74 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_56A.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_56A.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_56A.prot.xml' 0 sec job completed in 207 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_56.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_56.pep.xml' '20161205_Sample_56.pep.xml' -L'7'" file 1: 20161205_Sample_56.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_56.mzXML in msms_run_summary tag ... /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_11A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_11A.pep.xml' '20161205_Sample_11A.pep.xml' -L'7'" file 1: 20161205_Sample_11A.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_11A.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_11A.mzXML in msms_run_summary tag ... processed altogether 94326 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_11A.pep.xml command completed in 40 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_11A.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_11A.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 12 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_11A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 44720 2+, 36857 3+, 8743 4+, 1788 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 24260 Decoys, and 67848 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 60 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_11A.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_11A.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_11A (Comet)"... => Found 36264 hits. (0 decoys, 0 excluded) => Total so far: 36264 hits. (0 decoys, 0 excluded) command completed in 4 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_11A.pep.xml" command completed in 3 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_11A.pep.xml' 'interact-20161205_Sample_11A.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_11A.pep.xml... ...read in 0 1+, 20316 2+, 13129 3+, 2539 4+, 280 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 28123 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 9232 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10407 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10407 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10407 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10407 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10407 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10407 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6792 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10407 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.26997e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_11A.prot.xml command completed in 73 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_11A.prot.xml" Analyzing interact-20161205_Sample_11A.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_11A.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_11A.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_11A... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 12:40:14 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_11A.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_11A.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 12:40:19 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_11A.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_11A.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 12:40:19 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_11A.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_11A.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 12:40:19 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_11A.pep.xml' '20161205_Sample_11A.pep.xml' -L'7' 40 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_11A.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_11A.pep.xml' 'Cg-Giga_cont_AA.fa' 12 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_11A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 60 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_11A.pep.xml -d "DECOY_" 4 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_11A.pep.xml 3 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_11A.pep.xml' 'interact-20161205_Sample_11A.prot.xml' 73 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_11A.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_11A.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_11A.prot.xml' 0 sec job completed in 198 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_11.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_11.pep.xml' '20161205_Sample_11.pep.xml' -L'7'" file 1: 20161205_Sample_11.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_11.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_11.mzXML in msms_run_summary tag ... processed altogether 94172 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_11.pep.xml command completed in 40 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_11.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_11.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 12 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_11.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 43430 2+, 37127 3+, 9339 4+, 1888 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 24198 Decoys, and 67586 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 59 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_11.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_11.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_11 (Comet)"... => Found 36044 hits. (0 decoys, 0 excluded) => Total so far: 36044 hits. (0 decoys, 0 excluded) command completed in 4 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_11.pep.xml" command completed in 4 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_11.pep.xml' 'interact-20161205_Sample_11.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_11.pep.xml... ...read in 0 1+, 19797 2+, 13375 3+, 2606 4+, 266 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 27910 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 9088 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10283 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10283 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10283 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10283 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10283 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10283 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6736 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10283 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.23024e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_11.prot.xml command completed in 67 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_11.prot.xml" Analyzing interact-20161205_Sample_11.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_11.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_11.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_11... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 12:43:26 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_11.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_11.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 12:43:31 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_11.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_11.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 12:43:31 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_11.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_11.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 12:43:31 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_11.pep.xml' '20161205_Sample_11.pep.xml' -L'7' 40 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_11.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_11.pep.xml' 'Cg-Giga_cont_AA.fa' 12 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_11.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 59 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_11.pep.xml -d "DECOY_" 4 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_11.pep.xml 4 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_11.pep.xml' 'interact-20161205_Sample_11.prot.xml' 67 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_11.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_11.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_11.prot.xml' 0 sec job completed in 192 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_12A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_12A.pep.xml' '20161205_Sample_12A.pep.xml' -L'7'" file 1: 20161205_Sample_12A.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_12A.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_12A.mzXML in msms_run_summary tag ... processed altogether 97212 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_12A.pep.xml command completed in 41 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_12A.pep.xml'" command completed in 1 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_12A.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 12 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_12A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 46658 2+, 37909 3+, 8624 4+, 1888 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 23600 Decoys, and 71479 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 62 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_12A.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_12A.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_12A (Comet)"... => Found 40385 hits. (0 decoys, 0 excluded) => Total so far: 40385 hits. (0 decoys, 0 excluded) command completed in 5 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_12A.pep.xml" command completed in 3 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_12A.pep.xml' 'interact-20161205_Sample_12A.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_12A.pep.xml... ...read in 0 1+, 22888 2+, 14399 3+, 2753 4+, 345 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 31135 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 9715 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10935 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10935 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10935 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10935 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10935 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10935 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 7236 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10935 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.56119e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_12A.prot.xml command completed in 84 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_12A.prot.xml" Analyzing interact-20161205_Sample_12A.prot.xml ... command completed in 0 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_12A.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_12A.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_12A... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 12:46:59 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_12A.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_12A.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 12:47:05 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 6 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_12A.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_12A.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 12:47:05 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_12A.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_12A.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 12:47:05 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_12A.pep.xml' '20161205_Sample_12A.pep.xml' -L'7' 41 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_12A.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_12A.pep.xml' 'Cg-Giga_cont_AA.fa' 12 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_12A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 62 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_12A.pep.xml -d "DECOY_" 5 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_12A.pep.xml 3 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_12A.pep.xml' 'interact-20161205_Sample_12A.prot.xml' 84 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_12A.prot.xml 0 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_12A.pep.xml' 6 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_12A.prot.xml' 0 sec job completed in 214 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_12.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_12.pep.xml' '20161205_Sample_12.pep.xml' -L'7'" file 1: 20161205_Sample_12.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_12.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_12.mzXML in msms_run_summary tag ... processed altogether 97734 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_12.pep.xml command completed in 42 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_12.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_12.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 12 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_12.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 45383 2+, 38104 3+, 9606 4+, 2193 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 23385 Decoys, and 71901 Non-Decoys Iterations: .........10.........20....... model complete after 28 iterations command completed in 64 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_12.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_12.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_12 (Comet)"... => Found 41026 hits. (0 decoys, 0 excluded) => Total so far: 41026 hits. (0 decoys, 0 excluded) command completed in 5 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_12.pep.xml" command completed in 4 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_12.pep.xml' 'interact-20161205_Sample_12.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_12.pep.xml... ...read in 0 1+, 22738 2+, 14856 3+, 3070 4+, 362 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 31336 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 9726 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10958 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10958 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10958 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10958 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10958 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10958 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 7249 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10958 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=7.03042e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_12.prot.xml command completed in 84 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_12.prot.xml" Analyzing interact-20161205_Sample_12.prot.xml ... command completed in 0 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_12.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_12.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_12... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 12:50:36 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_12.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_12.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 12:50:42 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 6 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_12.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_12.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 12:50:42 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_12.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_12.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 12:50:42 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_12.pep.xml' '20161205_Sample_12.pep.xml' -L'7' 42 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_12.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_12.pep.xml' 'Cg-Giga_cont_AA.fa' 12 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_12.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 64 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_12.pep.xml -d "DECOY_" 5 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_12.pep.xml 4 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_12.pep.xml' 'interact-20161205_Sample_12.prot.xml' 84 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_12.prot.xml 0 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_12.pep.xml' 6 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_12.prot.xml' 0 sec job completed in 217 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_16A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_16A.pep.xml' '20161205_Sample_16A.pep.xml' -L'7'" file 1: 20161205_Sample_16A.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_16A.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_16A.mzXML in msms_run_summary tag ... processed altogether 97251 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_16A.pep.xml command completed in 42 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_16A.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_16A.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 11 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_16A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 48593 2+, 36211 3+, 8138 4+, 1994 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 25749 Decoys, and 69187 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 62 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_16A.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_16A.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_16A (Comet)"... => Found 35518 hits. (0 decoys, 0 excluded) => Total so far: 35518 hits. (0 decoys, 0 excluded) command completed in 4 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_16A.pep.xml" command completed in 4 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_16A.pep.xml' 'interact-20161205_Sample_16A.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_16A.pep.xml... ...read in 0 1+, 20598 2+, 12374 3+, 2286 4+, 260 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 27402 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 8951 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10126 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10126 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10126 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10126 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10126 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10126 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6576 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10126 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=5.71297e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_16A.prot.xml command completed in 65 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_16A.prot.xml" Analyzing interact-20161205_Sample_16A.prot.xml ... command completed in 0 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_16A.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_16A.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_16A... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 12:53:51 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_16A.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_16A.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 12:53:55 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_16A.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_16A.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 12:53:55 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_16A.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_16A.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 12:53:55 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_16A.pep.xml' '20161205_Sample_16A.pep.xml' -L'7' 42 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_16A.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_16A.pep.xml' 'Cg-Giga_cont_AA.fa' 11 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_16A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 62 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_16A.pep.xml -d "DECOY_" 4 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_16A.pep.xml 4 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_16A.pep.xml' 'interact-20161205_Sample_16A.prot.xml' 65 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_16A.prot.xml 0 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_16A.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_16A.prot.xml' 0 sec job completed in 193 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_16.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_16.pep.xml' '20161205_Sample_16.pep.xml' -L'7'" file 1: 20161205_Sample_16.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_16.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_16.mzXML in msms_run_summary tag ... processed altogether 98031 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_16.pep.xml command completed in 43 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_16.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_16.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 11 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_16.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 48949 2+, 35943 3+, 8554 4+, 2171 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 25823 Decoys, and 69794 Non-Decoys Iterations: .........10.........20....... model complete after 28 iterations command completed in 65 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_16.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_16.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_16 (Comet)"... => Found 36850 hits. (0 decoys, 0 excluded) => Total so far: 36850 hits. (0 decoys, 0 excluded) command completed in 4 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_16.pep.xml" command completed in 3 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_16.pep.xml' 'interact-20161205_Sample_16.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_16.pep.xml... ...read in 0 1+, 21550 2+, 12677 3+, 2371 4+, 252 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 27954 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 9230 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10438 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10438 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10438 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10438 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10438 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10438 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6794 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10438 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.26512e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_16.prot.xml command completed in 73 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_16.prot.xml" Analyzing interact-20161205_Sample_16.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_16.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_16.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_16... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 12:57:15 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_16.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_16.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 12:57:20 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_16.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_16.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 12:57:20 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_16.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_16.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 12:57:20 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_16.pep.xml' '20161205_Sample_16.pep.xml' -L'7' 43 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_16.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_16.pep.xml' 'Cg-Giga_cont_AA.fa' 11 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_16.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 65 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_16.pep.xml -d "DECOY_" 4 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_16.pep.xml 3 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_16.pep.xml' 'interact-20161205_Sample_16.prot.xml' 73 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_16.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_16.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_16.prot.xml' 0 sec job completed in 205 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_19A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_19A.pep.xml' '20161205_Sample_19A.pep.xml' -L'7'" file 1: 20161205_Sample_19A.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_19A.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_19A.mzXML in msms_run_summary tag ... processed altogether 96676 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_19A.pep.xml command completed in 41 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_19A.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_19A.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 12 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_19A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 47789 2+, 36675 3+, 8241 4+, 1684 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 23870 Decoys, and 70519 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 62 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_19A.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_19A.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_19A (Comet)"... => Found 39389 hits. (0 decoys, 0 excluded) => Total so far: 39389 hits. (0 decoys, 0 excluded) command completed in 5 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_19A.pep.xml" command completed in 3 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_19A.pep.xml' 'interact-20161205_Sample_19A.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_19A.pep.xml... ...read in 0 1+, 22867 2+, 13746 3+, 2482 4+, 294 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 30678 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 9771 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 11024 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 11024 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 11024 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 11024 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 11024 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 11024 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 11024 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 7170 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 11024 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.80245e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_19A.prot.xml command completed in 83 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_19A.prot.xml" Analyzing interact-20161205_Sample_19A.prot.xml ... command completed in 0 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_19A.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_19A.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_19A... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 13:00:46 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_19A.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_19A.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 13:00:51 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_19A.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_19A.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 13:00:51 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_19A.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_19A.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 13:00:52 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 1 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_19A.pep.xml' '20161205_Sample_19A.pep.xml' -L'7' 41 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_19A.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_19A.pep.xml' 'Cg-Giga_cont_AA.fa' 12 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_19A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 62 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_19A.pep.xml -d "DECOY_" 5 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_19A.pep.xml 3 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_19A.pep.xml' 'interact-20161205_Sample_19A.prot.xml' 83 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_19A.prot.xml 0 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_19A.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_19A.prot.xml' 1 sec job completed in 212 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_19.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_19.pep.xml' '20161205_Sample_19.pep.xml' -L'7'" file 1: 20161205_Sample_19.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_19.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_19.mzXML in msms_run_summary tag ... processed altogether 96696 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_19.pep.xml command completed in 41 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_19.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_19.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 11 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_19.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 45776 2+, 37507 3+, 8772 4+, 2074 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 23876 Decoys, and 70253 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 62 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_19.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_19.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_19 (Comet)"... => Found 38532 hits. (0 decoys, 0 excluded) => Total so far: 38532 hits. (0 decoys, 0 excluded) command completed in 4 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_19.pep.xml" command completed in 4 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_19.pep.xml' 'interact-20161205_Sample_19.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_19.pep.xml... ...read in 0 1+, 21616 2+, 13927 3+, 2671 4+, 318 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 29713 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 9267 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10467 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10467 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10467 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10467 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10467 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10467 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6944 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10467 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.36176e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_19.prot.xml command completed in 73 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_19.prot.xml" Analyzing interact-20161205_Sample_19.prot.xml ... command completed in 0 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_19.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_19.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_19... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 13:04:07 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_19.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_19.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 13:04:13 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 6 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_19.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_19.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 13:04:13 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_19.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_19.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 13:04:13 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_19.pep.xml' '20161205_Sample_19.pep.xml' -L'7' 41 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_19.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_19.pep.xml' 'Cg-Giga_cont_AA.fa' 11 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_19.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 62 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_19.pep.xml -d "DECOY_" 4 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_19.pep.xml 4 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_19.pep.xml' 'interact-20161205_Sample_19.prot.xml' 73 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_19.prot.xml 0 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_19.pep.xml' 6 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_19.prot.xml' 0 sec job completed in 201 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_1A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_1A.pep.xml' '20161205_Sample_1A.pep.xml' -L'7'" file 1: 20161205_Sample_1A.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_1A.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_1A.mzXML in msms_run_summary tag ... processed altogether 88832 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_1A.pep.xml command completed in 37 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_1A.pep.xml'" command completed in 1 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_1A.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 10 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_1A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 40726 2+, 35650 3+, 8460 4+, 1905 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 20638 Decoys, and 66103 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 58 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_1A.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_1A.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_1A (Comet)"... => Found 38786 hits. (0 decoys, 0 excluded) => Total so far: 38786 hits. (0 decoys, 0 excluded) command completed in 4 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_1A.pep.xml" command completed in 4 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_1A.pep.xml' 'interact-20161205_Sample_1A.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_1A.pep.xml... ...read in 0 1+, 21296 2+, 14386 3+, 2767 4+, 337 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 30559 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 9866 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 11145 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 11145 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 11145 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 11145 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 11145 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 11145 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 11145 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 7333 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 11145 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.43331e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_1A.prot.xml command completed in 81 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_1A.prot.xml" Analyzing interact-20161205_Sample_1A.prot.xml ... command completed in 0 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_1A.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_1A.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_1A... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 13:07:28 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_1A.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_1A.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 13:07:34 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 6 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_1A.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_1A.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 13:07:34 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_1A.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_1A.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 13:07:34 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_1A.pep.xml' '20161205_Sample_1A.pep.xml' -L'7' 37 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_1A.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_1A.pep.xml' 'Cg-Giga_cont_AA.fa' 10 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_1A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 58 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_1A.pep.xml -d "DECOY_" 4 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_1A.pep.xml 4 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_1A.pep.xml' 'interact-20161205_Sample_1A.prot.xml' 81 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_1A.prot.xml 0 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_1A.pep.xml' 6 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_1A.prot.xml' 0 sec job completed in 201 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_sample_1.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_sample_1.pep.xml' '20161205_sample_1.pep.xml' -L'7'" file 1: 20161205_sample_1.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_sample_1.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_sample_1.mzXML in msms_run_summary tag ... processed altogether 89352 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_sample_1.pep.xml command completed in 38 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_sample_1.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_sample_1.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 11 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_sample_1.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 38850 2+, 36561 3+, 9548 4+, 1969 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 20718 Decoys, and 66210 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 57 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_sample_1.pep.xml -d "DECOY_"" Analyzing interact-20161205_sample_1.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_sample_1 (Comet)"... => Found 38559 hits. (0 decoys, 0 excluded) => Total so far: 38559 hits. (0 decoys, 0 excluded) command completed in 5 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_sample_1.pep.xml" command completed in 3 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_sample_1.pep.xml' 'interact-20161205_sample_1.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_sample_1.pep.xml... ...read in 0 1+, 20196 2+, 14992 3+, 3059 4+, 312 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 29526 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 9601 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10869 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10869 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10869 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10869 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10869 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10869 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 7049 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10869 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.46199e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_sample_1.prot.xml command completed in 78 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_sample_1.prot.xml" Analyzing interact-20161205_sample_1.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_sample_1.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_sample_1.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_sample_1... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 13:10:47 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_sample_1.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_sample_1.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 13:10:52 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_sample_1.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_sample_1.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 13:10:52 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_sample_1.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_sample_1.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 13:10:52 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_sample_1.pep.xml' '20161205_sample_1.pep.xml' -L'7' 38 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_sample_1.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_sample_1.pep.xml' 'Cg-Giga_cont_AA.fa' 11 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_sample_1.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 57 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_sample_1.pep.xml -d "DECOY_" 5 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_sample_1.pep.xml 3 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_sample_1.pep.xml' 'interact-20161205_sample_1.prot.xml' 78 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_sample_1.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_sample_1.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_sample_1.prot.xml' 0 sec job completed in 198 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_20A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_20A.pep.xml' '20161205_Sample_20A.pep.xml' -L'7'" file 1: 20161205_Sample_20A.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_20A.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_20A.mzXML in msms_run_summary tag ... processed altogether 95228 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_20A.pep.xml command completed in 41 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_20A.pep.xml'" command completed in 1 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_20A.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 11 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_20A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 46465 2+, 36514 3+, 8199 4+, 1830 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 23377 Decoys, and 69631 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 61 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_20A.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_20A.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_20A (Comet)"... => Found 38722 hits. (0 decoys, 0 excluded) => Total so far: 38722 hits. (0 decoys, 0 excluded) command completed in 4 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_20A.pep.xml" command completed in 4 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_20A.pep.xml' 'interact-20161205_Sample_20A.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_20A.pep.xml... ...read in 0 1+, 22295 2+, 13628 3+, 2507 4+, 292 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 30137 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 9480 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10721 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10721 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10721 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10721 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10721 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10721 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 7044 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10721 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.25298e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_20A.prot.xml command completed in 74 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_20A.prot.xml" Analyzing interact-20161205_Sample_20A.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_20A.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_20A.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_20A... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 13:14:09 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_20A.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_20A.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 13:14:14 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_20A.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_20A.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 13:14:14 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_20A.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_20A.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 13:14:14 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_20A.pep.xml' '20161205_Sample_20A.pep.xml' -L'7' 41 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_20A.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_20A.pep.xml' 'Cg-Giga_cont_AA.fa' 11 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_20A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 61 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_20A.pep.xml -d "DECOY_" 4 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_20A.pep.xml 4 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_20A.pep.xml' 'interact-20161205_Sample_20A.prot.xml' 74 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_20A.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_20A.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_20A.prot.xml' 0 sec job completed in 202 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_20.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_20.pep.xml' '20161205_Sample_20.pep.xml' -L'7'" file 1: 20161205_Sample_20.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_20.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_20.mzXML in msms_run_summary tag ... processed altogether 96024 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_20.pep.xml command completed in 42 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_20.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_20.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 12 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_20.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 45260 2+, 37291 3+, 8911 4+, 2103 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 23326 Decoys, and 70239 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 62 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_20.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_20.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_20 (Comet)"... => Found 39081 hits. (0 decoys, 0 excluded) => Total so far: 39081 hits. (0 decoys, 0 excluded) command completed in 4 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_20.pep.xml" command completed in 4 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_20.pep.xml' 'interact-20161205_Sample_20.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_20.pep.xml... ...read in 0 1+, 21841 2+, 14190 3+, 2745 4+, 305 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 30033 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 9490 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10714 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10714 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10714 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10714 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10714 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10714 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6954 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10714 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.72818e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_20.prot.xml command completed in 78 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_20.prot.xml" Analyzing interact-20161205_Sample_20.prot.xml ... command completed in 0 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_20.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_20.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_20... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 13:17:36 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_20.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_20.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 13:17:41 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_20.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_20.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 13:17:42 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_20.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_20.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 13:17:42 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 1 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_20.pep.xml' '20161205_Sample_20.pep.xml' -L'7' 42 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_20.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_20.pep.xml' 'Cg-Giga_cont_AA.fa' 12 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_20.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 62 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_20.pep.xml -d "DECOY_" 4 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_20.pep.xml 4 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_20.pep.xml' 'interact-20161205_Sample_20.prot.xml' 78 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_20.prot.xml 0 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_20.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_20.prot.xml' 1 sec job completed in 208 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_24A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_24A.pep.xml' '20161205_Sample_24A.pep.xml' -L'7'" file 1: 20161205_Sample_24A.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_24A.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_24A.mzXML in msms_run_summary tag ... processed altogether 98362 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_24A.pep.xml command completed in 43 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_24A.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_24A.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 12 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_24A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 51761 2+, 35351 3+, 7260 4+, 1722 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 28255 Decoys, and 67839 Non-Decoys Iterations: .........10.........20....... model complete after 28 iterations command completed in 63 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_24A.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_24A.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_24A (Comet)"... => Found 32264 hits. (0 decoys, 0 excluded) => Total so far: 32264 hits. (0 decoys, 0 excluded) command completed in 4 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_24A.pep.xml" command completed in 3 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_24A.pep.xml' 'interact-20161205_Sample_24A.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_24A.pep.xml... ...read in 0 1+, 19792 2+, 10556 3+, 1728 4+, 188 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 25324 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 8917 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10132 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10132 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10132 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10132 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10132 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10132 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6488 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10132 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=5.66241e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_24A.prot.xml command completed in 63 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_24A.prot.xml" Analyzing interact-20161205_Sample_24A.prot.xml ... command completed in 0 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_24A.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_24A.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_24A... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 13:20:50 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_24A.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_24A.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 13:20:55 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_24A.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_24A.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 13:20:55 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_24A.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_24A.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 13:20:55 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_24A.pep.xml' '20161205_Sample_24A.pep.xml' -L'7' 43 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_24A.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_24A.pep.xml' 'Cg-Giga_cont_AA.fa' 12 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_24A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 63 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_24A.pep.xml -d "DECOY_" 4 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_24A.pep.xml 3 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_24A.pep.xml' 'interact-20161205_Sample_24A.prot.xml' 63 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_24A.prot.xml 0 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_24A.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_24A.prot.xml' 0 sec job completed in 193 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_24.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_24.pep.xml' '20161205_Sample_24.pep.xml' -L'7'" file 1: 20161205_Sample_24.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_24.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_24.mzXML in msms_run_summary tag ... processed altogether 97662 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_24.pep.xml command completed in 42 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_24.pep.xml'" command completed in 1 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_24.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 11 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_24.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 49257 2+, 35590 3+, 8382 4+, 1874 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 27881 Decoys, and 67222 Non-Decoys Iterations: .........10.........20....... model complete after 28 iterations command completed in 64 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_24.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_24.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_24 (Comet)"... => Found 32024 hits. (0 decoys, 0 excluded) => Total so far: 32024 hits. (0 decoys, 0 excluded) command completed in 4 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_24.pep.xml" command completed in 3 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_24.pep.xml' 'interact-20161205_Sample_24.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_24.pep.xml... ...read in 0 1+, 18981 2+, 10899 3+, 1983 4+, 161 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 24798 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 8520 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 9652 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9652 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9652 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9652 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9652 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9652 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6275 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 9652 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=5.76465e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_24.prot.xml command completed in 56 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_24.prot.xml" Analyzing interact-20161205_Sample_24.prot.xml ... command completed in 0 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_24.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_24.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_24... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 13:23:56 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_24.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_24.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 13:24:01 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_24.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_24.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 13:24:01 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_24.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_24.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 13:24:01 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_24.pep.xml' '20161205_Sample_24.pep.xml' -L'7' 42 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_24.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_24.pep.xml' 'Cg-Giga_cont_AA.fa' 11 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_24.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 64 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_24.pep.xml -d "DECOY_" 4 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_24.pep.xml 3 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_24.pep.xml' 'interact-20161205_Sample_24.prot.xml' 56 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_24.prot.xml 0 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_24.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_24.prot.xml' 0 sec job completed in 186 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_27A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_27A.pep.xml' '20161205_Sample_27A.pep.xml' -L'7'" file 1: 20161205_Sample_27A.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_27A.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_27A.mzXML in msms_run_summary tag ... processed altogether 96837 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_27A.pep.xml command completed in 42 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_27A.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_27A.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 12 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_27A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 51809 2+, 34018 3+, 7035 4+, 1634 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 29059 Decoys, and 65437 Non-Decoys Iterations: .........10.........20....... model complete after 28 iterations command completed in 63 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_27A.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_27A.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_27A (Comet)"... => Found 29418 hits. (0 decoys, 0 excluded) => Total so far: 29418 hits. (0 decoys, 0 excluded) command completed in 3 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_27A.pep.xml" command completed in 3 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_27A.pep.xml' 'interact-20161205_Sample_27A.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_27A.pep.xml... ...read in 0 1+, 17792 2+, 9779 3+, 1698 4+, 149 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 22967 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 8308 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 9428 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9428 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9428 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9428 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9428 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6047 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 9428 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=5.1794e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_27A.prot.xml command completed in 53 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_27A.prot.xml" Analyzing interact-20161205_Sample_27A.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_27A.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_27A.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_27A... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 13:26:58 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_27A.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_27A.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 13:27:02 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 4 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_27A.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_27A.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 13:27:02 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_27A.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_27A.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 13:27:02 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_27A.pep.xml' '20161205_Sample_27A.pep.xml' -L'7' 42 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_27A.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_27A.pep.xml' 'Cg-Giga_cont_AA.fa' 12 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_27A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 63 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_27A.pep.xml -d "DECOY_" 3 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_27A.pep.xml 3 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_27A.pep.xml' 'interact-20161205_Sample_27A.prot.xml' 53 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_27A.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_27A.pep.xml' 4 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_27A.prot.xml' 0 sec job completed in 181 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_27.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_27.pep.xml' '20161205_Sample_27.pep.xml' -L'7'" file 1: 20161205_Sample_27.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_27.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_27.mzXML in msms_run_summary tag ... processed altogether 97234 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_27.pep.xml command completed in 41 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_27.pep.xml'" command completed in 1 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_27.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 11 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_27.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 50325 2+, 34253 3+, 7983 4+, 1790 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 28716 Decoys, and 65635 Non-Decoys Iterations: .........10.........20....... model complete after 28 iterations command completed in 63 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_27.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_27.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_27 (Comet)"... => Found 29087 hits. (0 decoys, 0 excluded) => Total so far: 29087 hits. (0 decoys, 0 excluded) command completed in 4 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_27.pep.xml" command completed in 2 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_27.pep.xml' 'interact-20161205_Sample_27.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_27.pep.xml... ...read in 0 1+, 17245 2+, 9831 3+, 1852 4+, 159 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 22502 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 8410 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 9524 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9524 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9524 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9524 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9524 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9524 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6025 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 9524 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=5.53123e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_27.prot.xml command completed in 55 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_27.prot.xml" Analyzing interact-20161205_Sample_27.prot.xml ... command completed in 0 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_27.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_27.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_27... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 13:29:59 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_27.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_27.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 13:30:03 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 4 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_27.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_27.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 13:30:03 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_27.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_27.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 13:30:03 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_27.pep.xml' '20161205_Sample_27.pep.xml' -L'7' 41 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_27.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_27.pep.xml' 'Cg-Giga_cont_AA.fa' 11 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_27.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 63 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_27.pep.xml -d "DECOY_" 4 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_27.pep.xml 2 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_27.pep.xml' 'interact-20161205_Sample_27.prot.xml' 55 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_27.prot.xml 0 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_27.pep.xml' 4 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_27.prot.xml' 0 sec job completed in 181 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_28A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_28A.pep.xml' '20161205_Sample_28A.pep.xml' -L'7'" file 1: 20161205_Sample_28A.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_28A.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_28A.mzXML in msms_run_summary tag ... processed altogether 97504 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_28A.pep.xml command completed in 42 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_28A.pep.xml'" command completed in 1 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_28A.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 11 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_28A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 49043 2+, 36588 3+, 8050 4+, 1632 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 24853 Decoys, and 70460 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 63 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_28A.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_28A.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_28A (Comet)"... => Found 38326 hits. (0 decoys, 0 excluded) => Total so far: 38326 hits. (0 decoys, 0 excluded) command completed in 4 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_28A.pep.xml" command completed in 4 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_28A.pep.xml' 'interact-20161205_Sample_28A.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_28A.pep.xml... ...read in 0 1+, 22554 2+, 13088 3+, 2401 4+, 283 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 30065 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 9510 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10733 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10733 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10733 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10733 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10733 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10733 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 7019 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10733 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.53827e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_28A.prot.xml command completed in 76 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_28A.prot.xml" Analyzing interact-20161205_Sample_28A.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_28A.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_28A.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_28A... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 13:33:25 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_28A.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_28A.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 13:33:30 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_28A.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_28A.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 13:33:30 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_28A.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_28A.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 13:33:30 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_28A.pep.xml' '20161205_Sample_28A.pep.xml' -L'7' 42 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_28A.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_28A.pep.xml' 'Cg-Giga_cont_AA.fa' 11 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_28A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 63 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_28A.pep.xml -d "DECOY_" 4 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_28A.pep.xml 4 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_28A.pep.xml' 'interact-20161205_Sample_28A.prot.xml' 76 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_28A.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_28A.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_28A.prot.xml' 0 sec job completed in 207 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_28.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_28.pep.xml' '20161205_Sample_28.pep.xml' -L'7'" file 1: 20161205_Sample_28.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_28.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_28.mzXML in msms_run_summary tag ... processed altogether 96538 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_28.pep.xml command completed in 42 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_28.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_28.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 12 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_28.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 45950 2+, 37688 3+, 8780 4+, 1668 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 24120 Decoys, and 69966 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 62 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_28.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_28.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_28 (Comet)"... => Found 38767 hits. (0 decoys, 0 excluded) => Total so far: 38767 hits. (0 decoys, 0 excluded) command completed in 4 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_28.pep.xml" command completed in 4 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_28.pep.xml' 'interact-20161205_Sample_28.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_28.pep.xml... ...read in 0 1+, 21871 2+, 14179 3+, 2486 4+, 231 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 28468 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 9223 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10433 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10433 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10433 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10433 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10433 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10433 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10433 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6899 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10433 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.59475e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_28.prot.xml command completed in 74 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_28.prot.xml" Analyzing interact-20161205_Sample_28.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_28.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_28.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_28... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 13:36:49 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_28.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_28.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 13:36:54 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_28.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_28.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 13:36:54 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_28.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_28.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 13:36:54 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_28.pep.xml' '20161205_Sample_28.pep.xml' -L'7' 42 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_28.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_28.pep.xml' 'Cg-Giga_cont_AA.fa' 12 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_28.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 62 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_28.pep.xml -d "DECOY_" 4 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_28.pep.xml 4 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_28.pep.xml' 'interact-20161205_Sample_28.prot.xml' 74 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_28.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_28.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_28.prot.xml' 0 sec job completed in 204 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_32A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_32A.pep.xml' '20161205_Sample_32A.pep.xml' -L'7'" file 1: 20161205_Sample_32A.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_32A.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_32A.mzXML in msms_run_summary tag ... processed altogether 96330 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_32A.pep.xml command completed in 43 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_32A.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_32A.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 12 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_32A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 42588 2+, 38189 3+, 10676 4+, 2514 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 24823 Decoys, and 69144 Non-Decoys Iterations: .........10.........20....... model complete after 28 iterations command completed in 63 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_32A.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_32A.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_32A (Comet)"... => Found 36442 hits. (0 decoys, 0 excluded) => Total so far: 36442 hits. (0 decoys, 0 excluded) command completed in 4 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_32A.pep.xml" command completed in 4 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_32A.pep.xml' 'interact-20161205_Sample_32A.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_32A.pep.xml... ...read in 0 1+, 18882 2+, 13803 3+, 3299 4+, 458 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 28223 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 8903 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10051 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10051 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10051 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10051 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10051 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10051 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6497 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10051 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.67111e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_32A.prot.xml command completed in 73 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_32A.prot.xml" Analyzing interact-20161205_Sample_32A.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_32A.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_32A.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_32A... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 13:40:14 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_32A.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_32A.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 13:40:19 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_32A.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_32A.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 13:40:19 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_32A.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_32A.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 13:40:19 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_32A.pep.xml' '20161205_Sample_32A.pep.xml' -L'7' 43 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_32A.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_32A.pep.xml' 'Cg-Giga_cont_AA.fa' 12 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_32A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 63 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_32A.pep.xml -d "DECOY_" 4 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_32A.pep.xml 4 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_32A.pep.xml' 'interact-20161205_Sample_32A.prot.xml' 73 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_32A.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_32A.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_32A.prot.xml' 0 sec job completed in 205 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_32.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_32.pep.xml' '20161205_Sample_32.pep.xml' -L'7'" file 1: 20161205_Sample_32.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_32.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_32.mzXML in msms_run_summary tag ... processed altogether 96374 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_32.pep.xml command completed in 42 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_32.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_32.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 12 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_32.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 41072 2+, 38197 3+, 11287 4+, 3040 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 24764 Decoys, and 68832 Non-Decoys Iterations: .........10.........20....... model complete after 28 iterations command completed in 63 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_32.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_32.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_32 (Comet)"... => Found 36630 hits. (0 decoys, 0 excluded) => Total so far: 36630 hits. (0 decoys, 0 excluded) command completed in 5 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_32.pep.xml" command completed in 3 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_32.pep.xml' 'interact-20161205_Sample_32.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_32.pep.xml... ...read in 0 1+, 18804 2+, 13951 3+, 3406 4+, 469 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 28069 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 8923 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10086 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10086 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10086 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10086 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10086 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10086 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10086 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6577 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10086 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.69568e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_32.prot.xml command completed in 71 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_32.prot.xml" Analyzing interact-20161205_Sample_32.prot.xml ... command completed in 0 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_32.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_32.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_32... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 13:43:36 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_32.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_32.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 13:43:41 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 6 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_32.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_32.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 13:43:41 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_32.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_32.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 13:43:41 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_32.pep.xml' '20161205_Sample_32.pep.xml' -L'7' 42 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_32.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_32.pep.xml' 'Cg-Giga_cont_AA.fa' 12 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_32.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 63 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_32.pep.xml -d "DECOY_" 5 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_32.pep.xml 3 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_32.pep.xml' 'interact-20161205_Sample_32.prot.xml' 71 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_32.prot.xml 0 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_32.pep.xml' 6 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_32.prot.xml' 0 sec job completed in 202 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_35A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_35A.pep.xml' '20161205_Sample_35A.pep.xml' -L'7'" file 1: 20161205_Sample_35A.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_35A.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_35A.mzXML in msms_run_summary tag ... processed altogether 84905 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_35A.pep.xml command completed in 37 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_35A.pep.xml'" command completed in 1 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_35A.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 11 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_35A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 50986 2+, 23934 3+, 5657 4+, 1532 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 31793 Decoys, and 50316 Non-Decoys Iterations: .........10.........20......... model complete after 30 iterations command completed in 57 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_35A.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_35A.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_35A (Comet)"... => Found 11775 hits. (0 decoys, 0 excluded) => Total so far: 11775 hits. (0 decoys, 0 excluded) command completed in 2 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_35A.pep.xml" command completed in 1 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_35A.pep.xml' 'interact-20161205_Sample_35A.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_35A.pep.xml... ...read in 0 1+, 7335 2+, 3774 3+, 622 4+, 44 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 9506 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 5511 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 6335 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 6335 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 6335 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 6335 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 6335 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 6335 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 3754 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 6335 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=3.02076e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_35A.prot.xml command completed in 19 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_35A.prot.xml" Analyzing interact-20161205_Sample_35A.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_35A.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_35A.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_35A... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 13:45:50 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_35A.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_35A.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 13:45:51 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_35A.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_35A.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 13:45:52 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_35A.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_35A.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 13:45:52 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_35A.pep.xml' '20161205_Sample_35A.pep.xml' -L'7' 37 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_35A.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_35A.pep.xml' 'Cg-Giga_cont_AA.fa' 11 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_35A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 57 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_35A.pep.xml -d "DECOY_" 2 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_35A.pep.xml 1 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_35A.pep.xml' 'interact-20161205_Sample_35A.prot.xml' 19 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_35A.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_35A.pep.xml' 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_35A.prot.xml' 0 sec job completed in 131 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_35.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_35.pep.xml' '20161205_Sample_35.pep.xml' -L'7'" file 1: 20161205_Sample_35.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_35.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_35.mzXML in msms_run_summary tag ... processed altogether 86040 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_35.pep.xml command completed in 38 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_35.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_35.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 11 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_35.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 51121 2+, 24514 3+, 5904 4+, 1529 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 32318 Decoys, and 50750 Non-Decoys Iterations: .........10.........20........ model complete after 29 iterations command completed in 57 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_35.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_35.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_35 (Comet)"... => Found 12085 hits. (0 decoys, 0 excluded) => Total so far: 12085 hits. (0 decoys, 0 excluded) command completed in 1 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_35.pep.xml" command completed in 1 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_35.pep.xml' 'interact-20161205_Sample_35.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_35.pep.xml... ...read in 0 1+, 7521 2+, 3861 3+, 659 4+, 44 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 9682 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 5532 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 6370 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 6370 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 6370 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 6370 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 6370 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 3832 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 6370 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=2.9665e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_35.prot.xml command completed in 20 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_35.prot.xml" Analyzing interact-20161205_Sample_35.prot.xml ... command completed in 0 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_35.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_35.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_35... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 13:48:00 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_35.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_35.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 13:48:02 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 2 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_35.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_35.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 13:48:02 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_35.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_35.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 13:48:02 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_35.pep.xml' '20161205_Sample_35.pep.xml' -L'7' 38 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_35.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_35.pep.xml' 'Cg-Giga_cont_AA.fa' 11 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_35.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 57 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_35.pep.xml -d "DECOY_" 1 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_35.pep.xml 1 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_35.pep.xml' 'interact-20161205_Sample_35.prot.xml' 20 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_35.prot.xml 0 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_35.pep.xml' 2 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_35.prot.xml' 0 sec job completed in 130 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_36A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_36A.pep.xml' '20161205_Sample_36A.pep.xml' -L'7'" file 1: 20161205_Sample_36A.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_36A.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_36A.mzXML in msms_run_summary tag ... processed altogether 95308 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_36A.pep.xml command completed in 43 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_36A.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_36A.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 11 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_36A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 40309 2+, 38578 3+, 11250 4+, 2614 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 24958 Decoys, and 67793 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 61 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_36A.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_36A.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_36A (Comet)"... => Found 34901 hits. (0 decoys, 0 excluded) => Total so far: 34901 hits. (0 decoys, 0 excluded) command completed in 4 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_36A.pep.xml" command completed in 3 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_36A.pep.xml' 'interact-20161205_Sample_36A.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_36A.pep.xml... ...read in 0 1+, 17379 2+, 13691 3+, 3375 4+, 456 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 27008 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 8658 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 9803 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9803 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9803 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9803 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9803 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9803 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6378 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 9803 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.41576e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_36A.prot.xml command completed in 68 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_36A.prot.xml" Analyzing interact-20161205_Sample_36A.prot.xml ... command completed in 0 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_36A.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_36A.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_36A... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 13:51:12 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_36A.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_36A.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 13:51:17 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_36A.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_36A.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 13:51:17 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_36A.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_36A.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 13:51:17 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_36A.pep.xml' '20161205_Sample_36A.pep.xml' -L'7' 43 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_36A.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_36A.pep.xml' 'Cg-Giga_cont_AA.fa' 11 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_36A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 61 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_36A.pep.xml -d "DECOY_" 4 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_36A.pep.xml 3 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_36A.pep.xml' 'interact-20161205_Sample_36A.prot.xml' 68 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_36A.prot.xml 0 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_36A.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_36A.prot.xml' 0 sec job completed in 195 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_36.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_36.pep.xml' '20161205_Sample_36.pep.xml' -L'7'" file 1: 20161205_Sample_36.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_36.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_36.mzXML in msms_run_summary tag ... processed altogether 96434 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_36.pep.xml command completed in 43 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_36.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_36.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 12 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_36.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 41369 2+, 38063 3+, 11529 4+, 2865 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 24763 Decoys, and 69063 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 61 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_36.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_36.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_36 (Comet)"... => Found 36046 hits. (0 decoys, 0 excluded) => Total so far: 36046 hits. (0 decoys, 0 excluded) command completed in 4 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_36.pep.xml" command completed in 4 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_36.pep.xml' 'interact-20161205_Sample_36.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_36.pep.xml... ...read in 0 1+, 18447 2+, 13729 3+, 3409 4+, 461 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 27181 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 8978 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10162 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10162 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10162 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10162 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10162 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10162 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6555 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10162 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.5868e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_36.prot.xml command completed in 66 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_36.prot.xml" Analyzing interact-20161205_Sample_36.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_36.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_36.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_36... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 13:54:28 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_36.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_36.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 13:54:33 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_36.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_36.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 13:54:33 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_36.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_36.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 13:54:33 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_36.pep.xml' '20161205_Sample_36.pep.xml' -L'7' 43 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_36.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_36.pep.xml' 'Cg-Giga_cont_AA.fa' 12 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_36.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 61 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_36.pep.xml -d "DECOY_" 4 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_36.pep.xml 4 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_36.pep.xml' 'interact-20161205_Sample_36.prot.xml' 66 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_36.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_36.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_36.prot.xml' 0 sec job completed in 196 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_3A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_3A.pep.xml' '20161205_Sample_3A.pep.xml' -L'7'" file 1: 20161205_Sample_3A.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_3A.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_3A.mzXML in msms_run_summary tag ... processed altogether 90755 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_3A.pep.xml command completed in 39 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_3A.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_3A.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 11 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_3A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 40414 2+, 36656 3+, 9303 4+, 2006 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 22176 Decoys, and 66203 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 58 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_3A.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_3A.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_3A (Comet)"... => Found 36750 hits. (0 decoys, 0 excluded) => Total so far: 36750 hits. (0 decoys, 0 excluded) command completed in 4 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_3A.pep.xml" command completed in 4 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_3A.pep.xml' 'interact-20161205_Sample_3A.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_3A.pep.xml... ...read in 0 1+, 19285 2+, 14315 3+, 2811 4+, 339 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 28600 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 9274 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10465 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10465 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10465 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10465 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10465 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10465 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6871 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10465 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.18979e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_3A.prot.xml command completed in 74 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_3A.prot.xml" Analyzing interact-20161205_Sample_3A.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_3A.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_3A.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_3A... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 13:57:44 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_3A.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_3A.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 13:57:49 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_3A.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_3A.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 13:57:49 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_3A.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_3A.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 13:57:49 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_3A.pep.xml' '20161205_Sample_3A.pep.xml' -L'7' 39 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_3A.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_3A.pep.xml' 'Cg-Giga_cont_AA.fa' 11 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_3A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 58 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_3A.pep.xml -d "DECOY_" 4 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_3A.pep.xml 4 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_3A.pep.xml' 'interact-20161205_Sample_3A.prot.xml' 74 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_3A.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_3A.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_3A.prot.xml' 0 sec job completed in 196 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_3.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_3.pep.xml' '20161205_Sample_3.pep.xml' -L'7'" file 1: 20161205_Sample_3.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_3.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_3.mzXML in msms_run_summary tag ... processed altogether 90652 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_3.pep.xml command completed in 40 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_3.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_3.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 11 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_3.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 40560 2+, 36652 3+, 9207 4+, 1759 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 21962 Decoys, and 66216 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 57 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_3.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_3.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_3 (Comet)"... => Found 37017 hits. (0 decoys, 0 excluded) => Total so far: 37017 hits. (0 decoys, 0 excluded) command completed in 5 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_3.pep.xml" command completed in 3 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_3.pep.xml' 'interact-20161205_Sample_3.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_3.pep.xml... ...read in 0 1+, 19824 2+, 14236 3+, 2678 4+, 279 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 28869 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 9640 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10878 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10878 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10878 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10878 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10878 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10878 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10878 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 7043 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10878 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.4301e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_3.prot.xml command completed in 77 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_3.prot.xml" Analyzing interact-20161205_Sample_3.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_3.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_3.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_3... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 14:01:03 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_3.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_3.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 14:01:08 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_3.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_3.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 14:01:08 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_3.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_3.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 14:01:08 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_3.pep.xml' '20161205_Sample_3.pep.xml' -L'7' 40 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_3.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_3.pep.xml' 'Cg-Giga_cont_AA.fa' 11 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_3.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 57 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_3.pep.xml -d "DECOY_" 5 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_3.pep.xml 3 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_3.pep.xml' 'interact-20161205_Sample_3.prot.xml' 77 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_3.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_3.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_3.prot.xml' 0 sec job completed in 199 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_40A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_40A.pep.xml' '20161205_Sample_40A.pep.xml' -L'7'" file 1: 20161205_Sample_40A.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_40A.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_40A.mzXML in msms_run_summary tag ... processed altogether 92582 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_40A.pep.xml command completed in 41 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_40A.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_40A.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 11 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_40A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 37791 2+, 38172 3+, 11392 4+, 2885 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 24079 Decoys, and 66161 Non-Decoys Iterations: .........10.........20....... model complete after 28 iterations command completed in 61 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_40A.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_40A.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_40A (Comet)"... => Found 34538 hits. (0 decoys, 0 excluded) => Total so far: 34538 hits. (0 decoys, 0 excluded) command completed in 4 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_40A.pep.xml" command completed in 3 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_40A.pep.xml' 'interact-20161205_Sample_40A.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_40A.pep.xml... ...read in 0 1+, 16866 2+, 13806 3+, 3371 4+, 495 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 26672 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 8654 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 9788 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9788 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9788 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9788 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9788 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9788 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6376 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 9788 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.43797e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_40A.prot.xml command completed in 65 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_40A.prot.xml" Analyzing interact-20161205_Sample_40A.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_40A.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_40A.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_40A... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 14:04:14 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_40A.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_40A.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 14:04:19 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_40A.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_40A.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 14:04:19 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_40A.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_40A.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 14:04:19 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_40A.pep.xml' '20161205_Sample_40A.pep.xml' -L'7' 41 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_40A.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_40A.pep.xml' 'Cg-Giga_cont_AA.fa' 11 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_40A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 61 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_40A.pep.xml -d "DECOY_" 4 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_40A.pep.xml 3 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_40A.pep.xml' 'interact-20161205_Sample_40A.prot.xml' 65 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_40A.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_40A.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_40A.prot.xml' 0 sec job completed in 191 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_40.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_40.pep.xml' '20161205_Sample_40.pep.xml' -L'7'" file 1: 20161205_Sample_40.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_40.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_40.mzXML in msms_run_summary tag ... processed altogether 91598 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_40.pep.xml command completed in 39 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_40.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_40.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 12 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_40.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 37077 2+, 37293 3+, 11576 4+, 2977 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 23130 Decoys, and 65793 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 58 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_40.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_40.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_40 (Comet)"... => Found 35211 hits. (0 decoys, 0 excluded) => Total so far: 35211 hits. (0 decoys, 0 excluded) command completed in 4 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_40.pep.xml" command completed in 3 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_40.pep.xml' 'interact-20161205_Sample_40.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_40.pep.xml... ...read in 0 1+, 17269 2+, 14012 3+, 3458 4+, 472 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 26577 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 8806 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 9967 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9967 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9967 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9967 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9967 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9967 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6431 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 9967 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.44684e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_40.prot.xml command completed in 68 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_40.prot.xml" Analyzing interact-20161205_Sample_40.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_40.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_40.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_40... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 14:07:24 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_40.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_40.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 14:07:29 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_40.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_40.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 14:07:29 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_40.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_40.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 14:07:29 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_40.pep.xml' '20161205_Sample_40.pep.xml' -L'7' 39 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_40.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_40.pep.xml' 'Cg-Giga_cont_AA.fa' 12 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_40.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 58 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_40.pep.xml -d "DECOY_" 4 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_40.pep.xml 3 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_40.pep.xml' 'interact-20161205_Sample_40.prot.xml' 68 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_40.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_40.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_40.prot.xml' 0 sec job completed in 190 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_43A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_43A.pep.xml' '20161205_Sample_43A.pep.xml' -L'7'" file 1: 20161205_Sample_43A.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_43A.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_43A.mzXML in msms_run_summary tag ... processed altogether 88214 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_43A.pep.xml command completed in 38 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_43A.pep.xml'" command completed in 1 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_43A.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 10 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_43A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 54763 2+, 24387 3+, 5164 4+, 1568 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 31273 Decoys, and 54609 Non-Decoys Iterations: .........10.........20....... model complete after 28 iterations command completed in 57 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_43A.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_43A.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_43A (Comet)"... => Found 17061 hits. (0 decoys, 0 excluded) => Total so far: 17061 hits. (0 decoys, 0 excluded) command completed in 2 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_43A.pep.xml" command completed in 2 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_43A.pep.xml' 'interact-20161205_Sample_43A.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_43A.pep.xml... ...read in 0 1+, 11378 2+, 4970 3+, 652 4+, 61 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 13647 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 6626 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 7561 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 7561 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 7561 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 7561 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 7561 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 4631 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 7561 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=3.87219e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_43A.prot.xml command completed in 28 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_43A.prot.xml" Analyzing interact-20161205_Sample_43A.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_43A.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_43A.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_43A... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 14:09:48 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_43A.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_43A.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 14:09:50 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 2 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_43A.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_43A.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 14:09:50 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_43A.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_43A.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 14:09:50 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_43A.pep.xml' '20161205_Sample_43A.pep.xml' -L'7' 38 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_43A.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_43A.pep.xml' 'Cg-Giga_cont_AA.fa' 10 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_43A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 57 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_43A.pep.xml -d "DECOY_" 2 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_43A.pep.xml 2 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_43A.pep.xml' 'interact-20161205_Sample_43A.prot.xml' 28 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_43A.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_43A.pep.xml' 2 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_43A.prot.xml' 0 sec job completed in 141 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_43.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_43.pep.xml' '20161205_Sample_43.pep.xml' -L'7'" file 1: 20161205_Sample_43.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_43.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_43.mzXML in msms_run_summary tag ... processed altogether 89306 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_43.pep.xml command completed in 39 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_43.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_43.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 11 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_43.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 53897 2+, 25238 3+, 5735 4+, 1609 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 31763 Decoys, and 54716 Non-Decoys Iterations: .........10.........20........ model complete after 29 iterations command completed in 59 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_43.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_43.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_43 (Comet)"... => Found 16916 hits. (0 decoys, 0 excluded) => Total so far: 16916 hits. (0 decoys, 0 excluded) command completed in 2 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_43.pep.xml" command completed in 2 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_43.pep.xml' 'interact-20161205_Sample_43.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_43.pep.xml... ...read in 0 1+, 11128 2+, 5058 3+, 689 4+, 41 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 13526 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 6697 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 7634 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 7634 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 7634 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 7634 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 7634 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 7634 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 4670 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 7634 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=3.85772e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_43.prot.xml command completed in 28 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_43.prot.xml" Analyzing interact-20161205_Sample_43.prot.xml ... command completed in 0 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_43.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_43.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_43... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 14:12:11 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_43.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_43.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 14:12:14 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 3 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_43.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_43.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 14:12:14 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_43.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_43.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 14:12:14 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_43.pep.xml' '20161205_Sample_43.pep.xml' -L'7' 39 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_43.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_43.pep.xml' 'Cg-Giga_cont_AA.fa' 11 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_43.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 59 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_43.pep.xml -d "DECOY_" 2 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_43.pep.xml 2 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_43.pep.xml' 'interact-20161205_Sample_43.prot.xml' 28 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_43.prot.xml 0 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_43.pep.xml' 3 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_43.prot.xml' 0 sec job completed in 144 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_44A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_44A.pep.xml' '20161205_Sample_44A.pep.xml' -L'7'" file 1: 20161205_Sample_44A.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_44A.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_44A.mzXML in msms_run_summary tag ... processed altogether 93883 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_44A.pep.xml command completed in 41 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_44A.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_44A.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 11 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_44A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 49592 2+, 33069 3+, 6949 4+, 1762 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 26992 Decoys, and 64380 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 59 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_44A.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_44A.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_44A (Comet)"... => Found 29787 hits. (0 decoys, 0 excluded) => Total so far: 29787 hits. (0 decoys, 0 excluded) command completed in 4 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_44A.pep.xml" command completed in 3 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_44A.pep.xml' 'interact-20161205_Sample_44A.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_44A.pep.xml... ...read in 0 1+, 17794 2+, 10032 3+, 1767 4+, 194 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 23431 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 8667 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 9826 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9826 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9826 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9826 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9826 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6170 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 9826 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=5.49088e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_44A.prot.xml command completed in 53 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_44A.prot.xml" Analyzing interact-20161205_Sample_44A.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_44A.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_44A.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_44A... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 14:15:06 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_44A.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_44A.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 14:15:10 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 4 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_44A.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_44A.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 14:15:10 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_44A.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_44A.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 14:15:10 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_44A.pep.xml' '20161205_Sample_44A.pep.xml' -L'7' 41 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_44A.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_44A.pep.xml' 'Cg-Giga_cont_AA.fa' 11 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_44A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 59 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_44A.pep.xml -d "DECOY_" 4 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_44A.pep.xml 3 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_44A.pep.xml' 'interact-20161205_Sample_44A.prot.xml' 53 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_44A.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_44A.pep.xml' 4 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_44A.prot.xml' 0 sec job completed in 176 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_44.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_44.pep.xml' '20161205_Sample_44.pep.xml' -L'7'" file 1: 20161205_Sample_44.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_44.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_44.mzXML in msms_run_summary tag ... processed altogether 93502 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_44.pep.xml command completed in 41 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_44.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_44.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 12 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_44.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 47695 2+, 33399 3+, 7736 4+, 1993 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 26775 Decoys, and 64048 Non-Decoys Iterations: .........10.........20....... model complete after 28 iterations command completed in 60 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_44.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_44.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_44 (Comet)"... => Found 29529 hits. (0 decoys, 0 excluded) => Total so far: 29529 hits. (0 decoys, 0 excluded) command completed in 4 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_44.pep.xml" command completed in 2 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_44.pep.xml' 'interact-20161205_Sample_44.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_44.pep.xml... ...read in 0 1+, 17054 2+, 10374 3+, 1887 4+, 214 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 22936 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 8270 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 9380 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9380 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9380 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9380 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9380 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6007 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 9380 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=5.4995e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_44.prot.xml command completed in 55 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_44.prot.xml" Analyzing interact-20161205_Sample_44.prot.xml ... command completed in 0 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_44.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_44.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_44... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 14:18:04 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_44.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_44.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 14:18:08 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 4 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_44.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_44.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 14:18:09 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_44.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_44.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 14:18:09 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 1 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_44.pep.xml' '20161205_Sample_44.pep.xml' -L'7' 41 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_44.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_44.pep.xml' 'Cg-Giga_cont_AA.fa' 12 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_44.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 60 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_44.pep.xml -d "DECOY_" 4 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_44.pep.xml 2 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_44.pep.xml' 'interact-20161205_Sample_44.prot.xml' 55 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_44.prot.xml 0 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_44.pep.xml' 4 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_44.prot.xml' 1 sec job completed in 179 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_48A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_48A.pep.xml' '20161205_Sample_48A.pep.xml' -L'7'" file 1: 20161205_Sample_48A.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_48A.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_48A.mzXML in msms_run_summary tag ... processed altogether 100181 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_48A.pep.xml command completed in 43 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_48A.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_48A.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 12 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_48A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 50416 2+, 37052 3+, 8393 4+, 1951 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 24774 Decoys, and 73038 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 64 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_48A.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_48A.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_48A (Comet)"... => Found 40472 hits. (0 decoys, 0 excluded) => Total so far: 40472 hits. (0 decoys, 0 excluded) command completed in 5 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_48A.pep.xml" command completed in 4 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_48A.pep.xml' 'interact-20161205_Sample_48A.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_48A.pep.xml... ...read in 0 1+, 23782 2+, 13772 3+, 2588 4+, 330 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 30794 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 9658 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10947 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10947 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10947 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10947 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10947 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10947 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 7097 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10947 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.60396e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_48A.prot.xml command completed in 85 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_48A.prot.xml" Analyzing interact-20161205_Sample_48A.prot.xml ... command completed in 0 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_48A.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_48A.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_48A... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 14:21:42 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_48A.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_48A.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 14:21:48 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 6 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_48A.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_48A.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 14:21:48 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_48A.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_48A.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 14:21:48 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_48A.pep.xml' '20161205_Sample_48A.pep.xml' -L'7' 43 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_48A.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_48A.pep.xml' 'Cg-Giga_cont_AA.fa' 12 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_48A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 64 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_48A.pep.xml -d "DECOY_" 5 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_48A.pep.xml 4 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_48A.pep.xml' 'interact-20161205_Sample_48A.prot.xml' 85 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_48A.prot.xml 0 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_48A.pep.xml' 6 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_48A.prot.xml' 0 sec job completed in 219 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_48.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_48.pep.xml' '20161205_Sample_48.pep.xml' -L'7'" file 1: 20161205_Sample_48.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_48.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_48.mzXML in msms_run_summary tag ... processed altogether 97644 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_48.pep.xml command completed in 43 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_48.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_48.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 12 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_48.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 45652 2+, 37607 3+, 9291 4+, 2493 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 24124 Decoys, and 70919 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 62 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_48.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_48.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_48 (Comet)"... => Found 39279 hits. (0 decoys, 0 excluded) => Total so far: 39279 hits. (0 decoys, 0 excluded) command completed in 4 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_48.pep.xml" command completed in 4 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_48.pep.xml' 'interact-20161205_Sample_48.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_48.pep.xml... ...read in 0 1+, 21809 2+, 14241 3+, 2863 4+, 366 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 29381 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 9418 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10635 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10635 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10635 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10635 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10635 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10635 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6939 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10635 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.58989e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_48.prot.xml command completed in 77 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_48.prot.xml" Analyzing interact-20161205_Sample_48.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_48.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_48.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_48... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 14:25:11 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_48.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_48.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 14:25:16 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_48.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_48.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 14:25:16 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_48.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_48.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 14:25:16 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_48.pep.xml' '20161205_Sample_48.pep.xml' -L'7' 43 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_48.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_48.pep.xml' 'Cg-Giga_cont_AA.fa' 12 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_48.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 62 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_48.pep.xml -d "DECOY_" 4 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_48.pep.xml 4 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_48.pep.xml' 'interact-20161205_Sample_48.prot.xml' 77 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_48.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_48.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_48.prot.xml' 0 sec job completed in 208 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_4A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_4A.pep.xml' '20161205_Sample_4A.pep.xml' -L'7'" file 1: 20161205_Sample_4A.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_4A.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_4A.mzXML in msms_run_summary tag ... processed altogether 94919 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_4A.pep.xml command completed in 42 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_4A.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_4A.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 11 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_4A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 43668 2+, 37971 3+, 9039 4+, 2029 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 22749 Decoys, and 69958 Non-Decoys Iterations: .........10.........20....... model complete after 28 iterations command completed in 63 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_4A.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_4A.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_4A (Comet)"... => Found 40007 hits. (0 decoys, 0 excluded) => Total so far: 40007 hits. (0 decoys, 0 excluded) command completed in 5 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_4A.pep.xml" command completed in 3 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_4A.pep.xml' 'interact-20161205_Sample_4A.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_4A.pep.xml... ...read in 0 1+, 21885 2+, 14945 3+, 2830 4+, 347 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 30484 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 9681 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10913 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10913 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10913 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10913 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10913 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10913 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10913 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10913 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 7133 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10913 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.76596e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_4A.prot.xml command completed in 81 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_4A.prot.xml" Analyzing interact-20161205_Sample_4A.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_4A.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_4A.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_4A... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 14:28:42 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_4A.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_4A.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 14:28:47 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_4A.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_4A.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 14:28:47 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_4A.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_4A.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 14:28:47 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_4A.pep.xml' '20161205_Sample_4A.pep.xml' -L'7' 42 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_4A.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_4A.pep.xml' 'Cg-Giga_cont_AA.fa' 11 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_4A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 63 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_4A.pep.xml -d "DECOY_" 5 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_4A.pep.xml 3 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_4A.pep.xml' 'interact-20161205_Sample_4A.prot.xml' 81 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_4A.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_4A.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_4A.prot.xml' 0 sec job completed in 211 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_4.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_4.pep.xml' '20161205_Sample_4.pep.xml' -L'7'" file 1: 20161205_Sample_4.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_4.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_4.mzXML in msms_run_summary tag ... processed altogether 93878 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_4.pep.xml command completed in 42 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_4.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_4.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 11 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_4.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 42206 2+, 37669 3+, 9587 4+, 1957 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 22248 Decoys, and 69171 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 60 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_4.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_4.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_4 (Comet)"... => Found 40177 hits. (0 decoys, 0 excluded) => Total so far: 40177 hits. (0 decoys, 0 excluded) command completed in 5 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_4.pep.xml" command completed in 4 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_4.pep.xml' 'interact-20161205_Sample_4.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_4.pep.xml... ...read in 0 1+, 21522 2+, 15321 3+, 3039 4+, 295 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 30326 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 9806 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 11110 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 11110 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 11110 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 11110 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 11110 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 7154 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 11110 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.66618e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_4.prot.xml command completed in 79 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_4.prot.xml" Analyzing interact-20161205_Sample_4.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_4.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_4.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_4... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 14:32:09 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_4.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_4.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 14:32:14 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_4.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_4.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 14:32:15 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_4.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_4.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 14:32:15 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 1 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_4.pep.xml' '20161205_Sample_4.pep.xml' -L'7' 42 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_4.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_4.pep.xml' 'Cg-Giga_cont_AA.fa' 11 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_4.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 60 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_4.pep.xml -d "DECOY_" 5 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_4.pep.xml 4 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_4.pep.xml' 'interact-20161205_Sample_4.prot.xml' 79 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_4.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_4.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_4.prot.xml' 1 sec job completed in 208 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_51A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_51A.pep.xml' '20161205_Sample_51A.pep.xml' -L'7'" file 1: 20161205_Sample_51A.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_51A.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_51A.mzXML in msms_run_summary tag ... processed altogether 92551 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_51A.pep.xml command completed in 41 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_51A.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_51A.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 11 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_51A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 46433 2+, 33782 3+, 7885 4+, 1946 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 25868 Decoys, and 64178 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 59 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_51A.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_51A.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_51A (Comet)"... => Found 30941 hits. (0 decoys, 0 excluded) => Total so far: 30941 hits. (0 decoys, 0 excluded) command completed in 3 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_51A.pep.xml" command completed in 3 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_51A.pep.xml' 'interact-20161205_Sample_51A.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_51A.pep.xml... ...read in 0 1+, 17918 2+, 10810 3+, 1999 4+, 214 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 24311 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 8693 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 9800 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9800 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9800 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9800 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9800 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9800 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6297 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 9800 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=5.66329e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_51A.prot.xml command completed in 57 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_51A.prot.xml" Analyzing interact-20161205_Sample_51A.prot.xml ... command completed in 0 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_51A.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_51A.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_51A... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 14:35:09 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_51A.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_51A.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 14:35:14 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_51A.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_51A.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 14:35:14 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_51A.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_51A.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 14:35:14 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_51A.pep.xml' '20161205_Sample_51A.pep.xml' -L'7' 41 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_51A.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_51A.pep.xml' 'Cg-Giga_cont_AA.fa' 11 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_51A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 59 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_51A.pep.xml -d "DECOY_" 3 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_51A.pep.xml 3 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_51A.pep.xml' 'interact-20161205_Sample_51A.prot.xml' 57 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_51A.prot.xml 0 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_51A.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_51A.prot.xml' 0 sec job completed in 179 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_51.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_51.pep.xml' '20161205_Sample_51.pep.xml' -L'7'" file 1: 20161205_Sample_51.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_51.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_51.mzXML in msms_run_summary tag ... processed altogether 91634 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_51.pep.xml command completed in 40 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_51.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_51.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 12 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_51.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 44953 2+, 33385 3+, 8505 4+, 2016 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 25421 Decoys, and 63438 Non-Decoys Iterations: .........10.........20....... model complete after 28 iterations command completed in 59 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_51.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_51.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_51 (Comet)"... => Found 30941 hits. (0 decoys, 0 excluded) => Total so far: 30941 hits. (0 decoys, 0 excluded) command completed in 4 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_51.pep.xml" command completed in 3 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_51.pep.xml' 'interact-20161205_Sample_51.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_51.pep.xml... ...read in 0 1+, 17465 2+, 11195 3+, 2086 4+, 195 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 24253 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 8797 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 9963 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9963 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9963 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9963 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9963 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9963 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9963 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6337 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 9963 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=5.936e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_51.prot.xml command completed in 61 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_51.prot.xml" Analyzing interact-20161205_Sample_51.prot.xml ... command completed in 0 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_51.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_51.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_51... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 14:38:13 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_51.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_51.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 14:38:17 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 4 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_51.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_51.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 14:38:17 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_51.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_51.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 14:38:17 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_51.pep.xml' '20161205_Sample_51.pep.xml' -L'7' 40 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_51.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_51.pep.xml' 'Cg-Giga_cont_AA.fa' 12 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_51.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 59 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_51.pep.xml -d "DECOY_" 4 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_51.pep.xml 3 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_51.pep.xml' 'interact-20161205_Sample_51.prot.xml' 61 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_51.prot.xml 0 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_51.pep.xml' 4 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_51.prot.xml' 0 sec job completed in 183 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_52A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_52A.pep.xml' '20161205_Sample_52A.pep.xml' -L'7'" file 1: 20161205_Sample_52A.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_52A.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_52A.mzXML in msms_run_summary tag ... processed altogether 96309 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_52A.pep.xml command completed in 43 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_52A.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_52A.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 11 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_52A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 49269 2+, 34959 3+, 7592 4+, 2119 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 27015 Decoys, and 66924 Non-Decoys Iterations: .........10.........20....... model complete after 28 iterations command completed in 63 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_52A.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_52A.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_52A (Comet)"... => Found 32539 hits. (0 decoys, 0 excluded) => Total so far: 32539 hits. (0 decoys, 0 excluded) command completed in 3 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_52A.pep.xml" command completed in 4 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_52A.pep.xml' 'interact-20161205_Sample_52A.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_52A.pep.xml... ...read in 0 1+, 19012 2+, 11285 3+, 2012 4+, 230 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 25028 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 8942 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10093 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10093 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10093 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10093 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10093 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10093 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10093 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6411 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10093 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=5.65196e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_52A.prot.xml command completed in 63 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_52A.prot.xml" Analyzing interact-20161205_Sample_52A.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_52A.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_52A.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_52A... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 14:41:26 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_52A.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_52A.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 14:41:30 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 4 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_52A.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_52A.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 14:41:30 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_52A.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_52A.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 14:41:30 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_52A.pep.xml' '20161205_Sample_52A.pep.xml' -L'7' 43 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_52A.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_52A.pep.xml' 'Cg-Giga_cont_AA.fa' 11 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_52A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 63 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_52A.pep.xml -d "DECOY_" 3 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_52A.pep.xml 4 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_52A.pep.xml' 'interact-20161205_Sample_52A.prot.xml' 63 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_52A.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_52A.pep.xml' 4 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_52A.prot.xml' 0 sec job completed in 192 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_52.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_52.pep.xml' '20161205_Sample_52.pep.xml' -L'7'" file 1: 20161205_Sample_52.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_52.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_52.mzXML in msms_run_summary tag ... processed altogether 95741 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_52.pep.xml command completed in 43 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_52.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_52.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 12 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_52.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 48780 2+, 33467 3+, 8442 4+, 2188 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 26140 Decoys, and 66737 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 60 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_52.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_52.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_52 (Comet)"... => Found 32999 hits. (0 decoys, 0 excluded) => Total so far: 32999 hits. (0 decoys, 0 excluded) command completed in 3 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_52.pep.xml" command completed in 3 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_52.pep.xml' 'interact-20161205_Sample_52.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_52.pep.xml... ...read in 0 1+, 19669 2+, 10933 3+, 2201 4+, 196 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 25138 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 9114 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10307 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10307 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10307 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10307 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10307 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6490 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10307 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.36643e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_52.prot.xml command completed in 63 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_52.prot.xml" Analyzing interact-20161205_Sample_52.prot.xml ... command completed in 0 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_52.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_52.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_52... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 14:44:34 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_52.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_52.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 14:44:39 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_52.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_52.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 14:44:39 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_52.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_52.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 14:44:39 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_52.pep.xml' '20161205_Sample_52.pep.xml' -L'7' 43 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_52.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_52.pep.xml' 'Cg-Giga_cont_AA.fa' 12 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_52.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 60 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_52.pep.xml -d "DECOY_" 3 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_52.pep.xml 3 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_52.pep.xml' 'interact-20161205_Sample_52.prot.xml' 63 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_52.prot.xml 0 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_52.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_52.prot.xml' 0 sec job completed in 189 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_56A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_56A.pep.xml' '20161205_Sample_56A.pep.xml' -L'7'" file 1: 20161205_Sample_56A.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_56A.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_56A.mzXML in msms_run_summary tag ... processed altogether 99158 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_56A.pep.xml command completed in 45 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_56A.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_56A.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 12 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_56A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 46129 2+, 38164 3+, 9897 4+, 2412 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 25632 Decoys, and 70970 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 62 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_56A.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_56A.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_56A (Comet)"... => Found 36852 hits. (0 decoys, 0 excluded) => Total so far: 36852 hits. (0 decoys, 0 excluded) command completed in 5 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_56A.pep.xml" command completed in 3 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_56A.pep.xml' 'interact-20161205_Sample_56A.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_56A.pep.xml... ...read in 0 1+, 20081 2+, 13357 3+, 3028 4+, 386 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 28147 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 8987 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10185 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10185 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10185 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10185 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10185 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6530 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10185 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.60896e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_56A.prot.xml command completed in 74 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_56A.prot.xml" Analyzing interact-20161205_Sample_56A.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_56A.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_56A.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_56A... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 14:48:01 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_56A.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_56A.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 14:48:06 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_56A.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_56A.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 14:48:06 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_56A.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_56A.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 14:48:06 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_56A.pep.xml' '20161205_Sample_56A.pep.xml' -L'7' 45 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_56A.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_56A.pep.xml' 'Cg-Giga_cont_AA.fa' 12 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_56A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 62 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_56A.pep.xml -d "DECOY_" 5 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_56A.pep.xml 3 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_56A.pep.xml' 'interact-20161205_Sample_56A.prot.xml' 74 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_56A.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_56A.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_56A.prot.xml' 0 sec job completed in 207 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_56.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_56.pep.xml' '20161205_Sample_56.pep.xml' -L'7'" file 1: 20161205_Sample_56.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_56.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_56.mzXML in msms_run_summary tag ... processed altogether 98238 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_56.pep.xml command completed in 44 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_56.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_56.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 12 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_56.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 43221 2+, 39048 3+, 10464 4+, 2685 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 25290 Decoys, and 70128 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 62 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_56.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_56.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_56 (Comet)"... => Found 36827 hits. (0 decoys, 0 excluded) => Total so far: 36827 hits. (0 decoys, 0 excluded) command completed in 4 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_56.pep.xml" command completed in 4 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_56.pep.xml' 'interact-20161205_Sample_56.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_56.pep.xml... ...read in 0 1+, 19117 2+, 14057 3+, 3204 4+, 449 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 27814 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 8924 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10108 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10108 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10108 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10108 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10108 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10108 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6533 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10108 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.47967e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_56.prot.xml command completed in 73 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_56.prot.xml" Analyzing interact-20161205_Sample_56.prot.xml ... command completed in 0 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_56.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_56.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_56... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 14:51:25 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_56.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_56.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 14:51:30 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_56.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_56.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 14:51:30 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_56.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_56.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 14:51:30 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_56.pep.xml' '20161205_Sample_56.pep.xml' -L'7' 44 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_56.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_56.pep.xml' 'Cg-Giga_cont_AA.fa' 12 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_56.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 62 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_56.pep.xml -d "DECOY_" 4 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_56.pep.xml 4 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_56.pep.xml' 'interact-20161205_Sample_56.prot.xml' 73 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_56.prot.xml 0 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_56.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_56.prot.xml' 0 sec job completed in 204 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_8A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_8A.pep.xml' '20161205_Sample_8A.pep.xml' -L'7'" file 1: 20161205_Sample_8A.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_8A.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_8A.mzXML in msms_run_summary tag ... processed altogether 95365 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_8A.pep.xml command completed in 43 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_8A.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_8A.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 12 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_8A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 45084 2+, 37048 3+, 8963 4+, 2030 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 23440 Decoys, and 69685 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 61 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_8A.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_8A.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_8A (Comet)"... => Found 38682 hits. (0 decoys, 0 excluded) => Total so far: 38682 hits. (0 decoys, 0 excluded) command completed in 4 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_8A.pep.xml" command completed in 4 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_8A.pep.xml' 'interact-20161205_Sample_8A.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_8A.pep.xml... ...read in 0 1+, 21651 2+, 14011 3+, 2693 4+, 327 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 30016 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 9760 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10989 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10989 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10989 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10989 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10989 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10989 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 7125 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10989 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.67893e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_8A.prot.xml command completed in 76 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_8A.prot.xml" Analyzing interact-20161205_Sample_8A.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_8A.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_8A.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_8A... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 14:54:51 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_8A.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_8A.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 14:54:56 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_8A.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_8A.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 14:54:56 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_8A.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_8A.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 14:54:56 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_8A.pep.xml' '20161205_Sample_8A.pep.xml' -L'7' 43 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_8A.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_8A.pep.xml' 'Cg-Giga_cont_AA.fa' 12 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_8A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 61 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_8A.pep.xml -d "DECOY_" 4 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_8A.pep.xml 4 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_8A.pep.xml' 'interact-20161205_Sample_8A.prot.xml' 76 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_8A.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_8A.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_8A.prot.xml' 0 sec job completed in 206 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-20161205_Sample_8.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_8.pep.xml' '20161205_Sample_8.pep.xml' -L'7'" file 1: 20161205_Sample_8.pep.xml SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_8.mzXML in msms_run_summary tag ... SUCCESS: CORRECTED data file /home/sean/Documents/proteome/20161205_Sample_8.mzXML in msms_run_summary tag ... processed altogether 95433 results INFO: Results written to file: /home/sean/Documents/proteome/interact-20161205_Sample_8.pep.xml command completed in 42 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_8.pep.xml'" command completed in 0 sec running: "/usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_8.pep.xml' 'Cg-Giga_cont_AA.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 12 sec running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_8.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". (Comet) adding ACCMASS mixture distribution init with Comet trypsin MS Instrument info: Manufacturer: Thermo, Model: Orbitrap Fusion Lumos, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 43545 2+, 37816 3+, 9429 4+, 2223 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 23403 Decoys, and 69610 Non-Decoys Iterations: .........10.........20...... model complete after 27 iterations command completed in 61 sec running: "/usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_8.pep.xml -d "DECOY_"" Analyzing interact-20161205_Sample_8.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "/home/sean/Documents/proteome/20161205_Sample_8 (Comet)"... => Found 38230 hits. (0 decoys, 0 excluded) => Total so far: 38230 hits. (0 decoys, 0 excluded) command completed in 4 sec running: "/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_8.pep.xml" command completed in 4 sec running: "/usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_8.pep.xml' 'interact-20161205_Sample_8.prot.xml'" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/sean/Documents/proteome/interact-20161205_Sample_8.pep.xml... ...read in 0 1+, 20690 2+, 14294 3+, 2882 4+, 364 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 29333 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database Cg-Giga_cont_AA.fa .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:..... Total: 40751 Computing degenerate peptides for 9196 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 10385 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10385 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10385 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10385 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10385 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 10385 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6873 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 10385 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=6.67256e-06, db_size=40397625 Finished. Results written to: /home/sean/Documents/proteome/interact-20161205_Sample_8.prot.xml command completed in 76 sec running: "/usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_8.prot.xml" Analyzing interact-20161205_Sample_8.prot.xml ... command completed in 1 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_8.pep.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_8.pep.xml - in ms run: /home/sean/Documents/proteome/20161205_Sample_8... ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 14:58:16 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_8.pep.xml is pepxml Found fval (+1) model... Found ntt (+1) model... Found nmc (+1) model... Found AccurateMassModel ('+1') model... Found IsoMassDiff (+1) model... Found fval (+2) model... Found ntt (+2) model... Found nmc (+2) model... Found AccurateMassModel ('+2') model... Found IsoMassDiff (+2) model... Found fval (+3) model... Found ntt (+3) model... Found nmc (+3) model... Found AccurateMassModel ('+3') model... Found IsoMassDiff (+3) model... Found fval (+4) model... Found ntt (+4) model... Found nmc (+4) model... Found AccurateMassModel ('+4') model... Found IsoMassDiff (+4) model... Found fval (+5) model... Found ntt (+5) model... Found nmc (+5) model... Found AccurateMassModel ('+5') model... Found IsoMassDiff (+5) model... Found fval (+6) model... Found ntt (+6) model... Found nmc (+6) model... Found AccurateMassModel ('+6') model... Found IsoMassDiff (+6) model... Found fval (+7) model... Found ntt (+7) model... Found nmc (+7) model... Found AccurateMassModel ('+7') model... Found IsoMassDiff (+7) model... --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_8.pep-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 14:58:21 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 5 sec running: "/usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_8.prot.xml'" File: /home/sean/Documents/proteome/interact-20161205_Sample_8.prot.xml ------------------------------------------------------------------------------- TPP DASHBOARD -- started at Mon Feb 20 14:58:21 2017 ------------------------------------------------------------------------------- File /home/sean/Documents/proteome/interact-20161205_Sample_8.prot.xml is protxml Found end of header --> Trying to write file /home/sean/Documents/proteome/interact-20161205_Sample_8.prot-MODELS.html ------------------------------------------------------------------------------- Finished at Mon Feb 20 14:58:21 2017 with 0 errors. ------------------------------------------------------------------------------- command completed in 0 sec /usr/tpp_install/tpp/bin/InteractParser 'interact-20161205_Sample_8.pep.xml' '20161205_Sample_8.pep.xml' -L'7' 42 sec /usr/tpp_install/tpp/bin/DatabaseParser 'interact-20161205_Sample_8.pep.xml' /usr/tpp_install/tpp/bin/RefreshParser 'interact-20161205_Sample_8.pep.xml' 'Cg-Giga_cont_AA.fa' 12 sec /usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-20161205_Sample_8.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS 61 sec /usr/tpp_install/tpp/bin/ProphetModels.pl -i interact-20161205_Sample_8.pep.xml -d "DECOY_" 4 sec /usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -I /home/sean/Documents/proteome/interact-20161205_Sample_8.pep.xml 4 sec /usr/tpp_install/tpp/bin/ProteinProphet 'interact-20161205_Sample_8.pep.xml' 'interact-20161205_Sample_8.prot.xml' 76 sec /usr/tpp_install/tpp/bin/ProtProphModels.pl -i interact-20161205_Sample_8.prot.xml 1 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_8.pep.xml' 5 sec /usr/tpp_install/tpp/bin/tpp_models.pl '/home/sean/Documents/proteome/interact-20161205_Sample_8.prot.xml' 0 sec job completed in 205 sec /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_11A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_11A.pep.xml' 'interact-20161205_Sample_11A.pep.xml' -L'7'" Skipping file interact-20161205_Sample_11A.pep.xml, which already contains peptideprophet results ... processed altogether 0 results ERROR: output file created, /home/sean/Documents/proteome/interact-interact-20161205_Sample_11A.pep.xml, appears incomplete. Please check the input files for completeness. INFO: Results written to file: /home/sean/Documents/proteome/interact-interact-20161205_Sample_11A.pep.xml command completed in 0 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-interact-20161205_Sample_11A.pep.xml'" command completed in 0 sec No single database specified (by -D option or in .pep.xml file). RefreshParser skipped. running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_11A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN Error: file update failed (did not find closing tag ""), check file interact-interact-20161205_Sample_11A.pep.xml.tmp.tHDjQ3 for completeness error: no peptideprophet data written to file interact-interact-20161205_Sample_11A.pep.xml command "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_11A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" exited with non-zero exit code: 256 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_11A.prot.xml.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_11A.prot.xml.pep.xml' 'interact-20161205_Sample_11A.prot.xml.pep.xml' -L'7'" terminate called after throwing an instance of 'boost::exception_detail::clone_impl >' what(): failed opening file: No such file or directory: iostream error Aborted (core dumped) command "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_11A.prot.xml.pep.xml' 'interact-20161205_Sample_11A.prot.xml.pep.xml' -L'7'" exited with non-zero exit code: 34304 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_11.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_11.pep.xml' 'interact-20161205_Sample_11.pep.xml' -L'7'" Skipping file interact-20161205_Sample_11.pep.xml, which already contains peptideprophet results ... processed altogether 0 results ERROR: output file created, /home/sean/Documents/proteome/interact-interact-20161205_Sample_11.pep.xml, appears incomplete. Please check the input files for completeness. INFO: Results written to file: /home/sean/Documents/proteome/interact-interact-20161205_Sample_11.pep.xml command completed in 0 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-interact-20161205_Sample_11.pep.xml'" command completed in 0 sec No single database specified (by -D option or in .pep.xml file). RefreshParser skipped. running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_11.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN Error: file update failed (did not find closing tag ""), check file interact-interact-20161205_Sample_11.pep.xml.tmp.J0myNM for completeness error: no peptideprophet data written to file interact-interact-20161205_Sample_11.pep.xml command "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_11.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" exited with non-zero exit code: 256 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_11.prot.xml.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_11.prot.xml.pep.xml' 'interact-20161205_Sample_11.prot.xml.pep.xml' -L'7'" terminate called after throwing an instance of 'boost::exception_detail::clone_impl >' what(): failed opening file: No such file or directory: iostream error Aborted (core dumped) command "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_11.prot.xml.pep.xml' 'interact-20161205_Sample_11.prot.xml.pep.xml' -L'7'" exited with non-zero exit code: 34304 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_12A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_12A.pep.xml' 'interact-20161205_Sample_12A.pep.xml' -L'7'" Skipping file interact-20161205_Sample_12A.pep.xml, which already contains peptideprophet results ... processed altogether 0 results ERROR: output file created, /home/sean/Documents/proteome/interact-interact-20161205_Sample_12A.pep.xml, appears incomplete. Please check the input files for completeness. INFO: Results written to file: /home/sean/Documents/proteome/interact-interact-20161205_Sample_12A.pep.xml command completed in 0 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-interact-20161205_Sample_12A.pep.xml'" command completed in 0 sec No single database specified (by -D option or in .pep.xml file). RefreshParser skipped. running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_12A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN Error: file update failed (did not find closing tag ""), check file interact-interact-20161205_Sample_12A.pep.xml.tmp.NBZRoa for completeness error: no peptideprophet data written to file interact-interact-20161205_Sample_12A.pep.xml command "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_12A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" exited with non-zero exit code: 256 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_12A.prot.xml.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_12A.prot.xml.pep.xml' 'interact-20161205_Sample_12A.prot.xml.pep.xml' -L'7'" terminate called after throwing an instance of 'boost::exception_detail::clone_impl >' what(): failed opening file: No such file or directory: iostream error Aborted (core dumped) command "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_12A.prot.xml.pep.xml' 'interact-20161205_Sample_12A.prot.xml.pep.xml' -L'7'" exited with non-zero exit code: 34304 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_12.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_12.pep.xml' 'interact-20161205_Sample_12.pep.xml' -L'7'" Skipping file interact-20161205_Sample_12.pep.xml, which already contains peptideprophet results ... processed altogether 0 results ERROR: output file created, /home/sean/Documents/proteome/interact-interact-20161205_Sample_12.pep.xml, appears incomplete. Please check the input files for completeness. INFO: Results written to file: /home/sean/Documents/proteome/interact-interact-20161205_Sample_12.pep.xml command completed in 0 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-interact-20161205_Sample_12.pep.xml'" command completed in 0 sec No single database specified (by -D option or in .pep.xml file). RefreshParser skipped. running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_12.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN Error: file update failed (did not find closing tag ""), check file interact-interact-20161205_Sample_12.pep.xml.tmp.eoii5y for completeness error: no peptideprophet data written to file interact-interact-20161205_Sample_12.pep.xml command "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_12.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" exited with non-zero exit code: 256 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_12.prot.xml.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_12.prot.xml.pep.xml' 'interact-20161205_Sample_12.prot.xml.pep.xml' -L'7'" terminate called after throwing an instance of 'boost::exception_detail::clone_impl >' what(): failed opening file: No such file or directory: iostream error Aborted (core dumped) command "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_12.prot.xml.pep.xml' 'interact-20161205_Sample_12.prot.xml.pep.xml' -L'7'" exited with non-zero exit code: 34304 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_16A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_16A.pep.xml' 'interact-20161205_Sample_16A.pep.xml' -L'7'" Skipping file interact-20161205_Sample_16A.pep.xml, which already contains peptideprophet results ... processed altogether 0 results ERROR: output file created, /home/sean/Documents/proteome/interact-interact-20161205_Sample_16A.pep.xml, appears incomplete. Please check the input files for completeness. INFO: Results written to file: /home/sean/Documents/proteome/interact-interact-20161205_Sample_16A.pep.xml command completed in 0 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-interact-20161205_Sample_16A.pep.xml'" command completed in 0 sec No single database specified (by -D option or in .pep.xml file). RefreshParser skipped. running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_16A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN Error: file update failed (did not find closing tag ""), check file interact-interact-20161205_Sample_16A.pep.xml.tmp.GAwRcX for completeness error: no peptideprophet data written to file interact-interact-20161205_Sample_16A.pep.xml command "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_16A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" exited with non-zero exit code: 256 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_16A.prot.xml.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_16A.prot.xml.pep.xml' 'interact-20161205_Sample_16A.prot.xml.pep.xml' -L'7'" terminate called after throwing an instance of 'boost::exception_detail::clone_impl >' what(): failed opening file: No such file or directory: iostream error Aborted (core dumped) command "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_16A.prot.xml.pep.xml' 'interact-20161205_Sample_16A.prot.xml.pep.xml' -L'7'" exited with non-zero exit code: 34304 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_16.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_16.pep.xml' 'interact-20161205_Sample_16.pep.xml' -L'7'" Skipping file interact-20161205_Sample_16.pep.xml, which already contains peptideprophet results ... processed altogether 0 results ERROR: output file created, /home/sean/Documents/proteome/interact-interact-20161205_Sample_16.pep.xml, appears incomplete. Please check the input files for completeness. INFO: Results written to file: /home/sean/Documents/proteome/interact-interact-20161205_Sample_16.pep.xml command completed in 0 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-interact-20161205_Sample_16.pep.xml'" command completed in 0 sec No single database specified (by -D option or in .pep.xml file). RefreshParser skipped. running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_16.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN Error: file update failed (did not find closing tag ""), check file interact-interact-20161205_Sample_16.pep.xml.tmp.kyyQxe for completeness error: no peptideprophet data written to file interact-interact-20161205_Sample_16.pep.xml command "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_16.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" exited with non-zero exit code: 256 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_16.prot.xml.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_16.prot.xml.pep.xml' 'interact-20161205_Sample_16.prot.xml.pep.xml' -L'7'" terminate called after throwing an instance of 'boost::exception_detail::clone_impl >' what(): failed opening file: No such file or directory: iostream error Aborted (core dumped) command "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_16.prot.xml.pep.xml' 'interact-20161205_Sample_16.prot.xml.pep.xml' -L'7'" exited with non-zero exit code: 34304 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_19A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_19A.pep.xml' 'interact-20161205_Sample_19A.pep.xml' -L'7'" Skipping file interact-20161205_Sample_19A.pep.xml, which already contains peptideprophet results ... processed altogether 0 results ERROR: output file created, /home/sean/Documents/proteome/interact-interact-20161205_Sample_19A.pep.xml, appears incomplete. Please check the input files for completeness. INFO: Results written to file: /home/sean/Documents/proteome/interact-interact-20161205_Sample_19A.pep.xml command completed in 0 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-interact-20161205_Sample_19A.pep.xml'" command completed in 0 sec No single database specified (by -D option or in .pep.xml file). RefreshParser skipped. running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_19A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN Error: file update failed (did not find closing tag ""), check file interact-interact-20161205_Sample_19A.pep.xml.tmp.avNjPz for completeness error: no peptideprophet data written to file interact-interact-20161205_Sample_19A.pep.xml command "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_19A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" exited with non-zero exit code: 256 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_19A.prot.xml.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_19A.prot.xml.pep.xml' 'interact-20161205_Sample_19A.prot.xml.pep.xml' -L'7'" terminate called after throwing an instance of 'boost::exception_detail::clone_impl >' what(): failed opening file: No such file or directory: iostream error Aborted (core dumped) command "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_19A.prot.xml.pep.xml' 'interact-20161205_Sample_19A.prot.xml.pep.xml' -L'7'" exited with non-zero exit code: 34304 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_19.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_19.pep.xml' 'interact-20161205_Sample_19.pep.xml' -L'7'" Skipping file interact-20161205_Sample_19.pep.xml, which already contains peptideprophet results ... processed altogether 0 results ERROR: output file created, /home/sean/Documents/proteome/interact-interact-20161205_Sample_19.pep.xml, appears incomplete. Please check the input files for completeness. INFO: Results written to file: /home/sean/Documents/proteome/interact-interact-20161205_Sample_19.pep.xml command completed in 0 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-interact-20161205_Sample_19.pep.xml'" command completed in 0 sec No single database specified (by -D option or in .pep.xml file). RefreshParser skipped. running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_19.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN Error: file update failed (did not find closing tag ""), check file interact-interact-20161205_Sample_19.pep.xml.tmp.ujFRWX for completeness error: no peptideprophet data written to file interact-interact-20161205_Sample_19.pep.xml command "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_19.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" exited with non-zero exit code: 256 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_19.prot.xml.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_19.prot.xml.pep.xml' 'interact-20161205_Sample_19.prot.xml.pep.xml' -L'7'" terminate called after throwing an instance of 'boost::exception_detail::clone_impl >' what(): failed opening file: No such file or directory: iostream error Aborted (core dumped) command "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_19.prot.xml.pep.xml' 'interact-20161205_Sample_19.prot.xml.pep.xml' -L'7'" exited with non-zero exit code: 34304 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_1A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_1A.pep.xml' 'interact-20161205_Sample_1A.pep.xml' -L'7'" Skipping file interact-20161205_Sample_1A.pep.xml, which already contains peptideprophet results ... processed altogether 0 results ERROR: output file created, /home/sean/Documents/proteome/interact-interact-20161205_Sample_1A.pep.xml, appears incomplete. Please check the input files for completeness. INFO: Results written to file: /home/sean/Documents/proteome/interact-interact-20161205_Sample_1A.pep.xml command completed in 0 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-interact-20161205_Sample_1A.pep.xml'" command completed in 0 sec No single database specified (by -D option or in .pep.xml file). RefreshParser skipped. running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_1A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN Error: file update failed (did not find closing tag ""), check file interact-interact-20161205_Sample_1A.pep.xml.tmp.AXL0ln for completeness error: no peptideprophet data written to file interact-interact-20161205_Sample_1A.pep.xml command "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_1A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" exited with non-zero exit code: 256 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_1A.prot.xml.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_1A.prot.xml.pep.xml' 'interact-20161205_Sample_1A.prot.xml.pep.xml' -L'7'" terminate called after throwing an instance of 'boost::exception_detail::clone_impl >' what(): failed opening file: No such file or directory: iostream error Aborted (core dumped) command "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_1A.prot.xml.pep.xml' 'interact-20161205_Sample_1A.prot.xml.pep.xml' -L'7'" exited with non-zero exit code: 34304 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_sample_1.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_sample_1.pep.xml' 'interact-20161205_sample_1.pep.xml' -L'7'" Skipping file interact-20161205_sample_1.pep.xml, which already contains peptideprophet results ... processed altogether 0 results ERROR: output file created, /home/sean/Documents/proteome/interact-interact-20161205_sample_1.pep.xml, appears incomplete. Please check the input files for completeness. INFO: Results written to file: /home/sean/Documents/proteome/interact-interact-20161205_sample_1.pep.xml command completed in 0 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-interact-20161205_sample_1.pep.xml'" command completed in 0 sec No single database specified (by -D option or in .pep.xml file). RefreshParser skipped. running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_sample_1.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN Error: file update failed (did not find closing tag ""), check file interact-interact-20161205_sample_1.pep.xml.tmp.oyFZYL for completeness error: no peptideprophet data written to file interact-interact-20161205_sample_1.pep.xml command "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_sample_1.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" exited with non-zero exit code: 256 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_sample_1.prot.xml.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_sample_1.prot.xml.pep.xml' 'interact-20161205_sample_1.prot.xml.pep.xml' -L'7'" terminate called after throwing an instance of 'boost::exception_detail::clone_impl >' what(): failed opening file: No such file or directory: iostream error Aborted (core dumped) command "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_sample_1.prot.xml.pep.xml' 'interact-20161205_sample_1.prot.xml.pep.xml' -L'7'" exited with non-zero exit code: 34304 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_20A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_20A.pep.xml' 'interact-20161205_Sample_20A.pep.xml' -L'7'" Skipping file interact-20161205_Sample_20A.pep.xml, which already contains peptideprophet results ... processed altogether 0 results ERROR: output file created, /home/sean/Documents/proteome/interact-interact-20161205_Sample_20A.pep.xml, appears incomplete. Please check the input files for completeness. INFO: Results written to file: /home/sean/Documents/proteome/interact-interact-20161205_Sample_20A.pep.xml command completed in 1 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-interact-20161205_Sample_20A.pep.xml'" command completed in 0 sec No single database specified (by -D option or in .pep.xml file). RefreshParser skipped. running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_20A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN Error: file update failed (did not find closing tag ""), check file interact-interact-20161205_Sample_20A.pep.xml.tmp.JZxs3Z for completeness error: no peptideprophet data written to file interact-interact-20161205_Sample_20A.pep.xml command "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_20A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" exited with non-zero exit code: 256 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_20A.prot.xml.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_20A.prot.xml.pep.xml' 'interact-20161205_Sample_20A.prot.xml.pep.xml' -L'7'" terminate called after throwing an instance of 'boost::exception_detail::clone_impl >' what(): failed opening file: No such file or directory: iostream error Aborted (core dumped) command "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_20A.prot.xml.pep.xml' 'interact-20161205_Sample_20A.prot.xml.pep.xml' -L'7'" exited with non-zero exit code: 34304 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_20.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_20.pep.xml' 'interact-20161205_Sample_20.pep.xml' -L'7'" Skipping file interact-20161205_Sample_20.pep.xml, which already contains peptideprophet results ... processed altogether 0 results ERROR: output file created, /home/sean/Documents/proteome/interact-interact-20161205_Sample_20.pep.xml, appears incomplete. Please check the input files for completeness. INFO: Results written to file: /home/sean/Documents/proteome/interact-interact-20161205_Sample_20.pep.xml command completed in 0 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-interact-20161205_Sample_20.pep.xml'" command completed in 0 sec No single database specified (by -D option or in .pep.xml file). RefreshParser skipped. running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_20.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN Error: file update failed (did not find closing tag ""), check file interact-interact-20161205_Sample_20.pep.xml.tmp.us5YMn for completeness error: no peptideprophet data written to file interact-interact-20161205_Sample_20.pep.xml command "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_20.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" exited with non-zero exit code: 256 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_20.prot.xml.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_20.prot.xml.pep.xml' 'interact-20161205_Sample_20.prot.xml.pep.xml' -L'7'" terminate called after throwing an instance of 'boost::exception_detail::clone_impl >' what(): failed opening file: No such file or directory: iostream error Aborted (core dumped) command "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_20.prot.xml.pep.xml' 'interact-20161205_Sample_20.prot.xml.pep.xml' -L'7'" exited with non-zero exit code: 34304 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_24A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_24A.pep.xml' 'interact-20161205_Sample_24A.pep.xml' -L'7'" Skipping file interact-20161205_Sample_24A.pep.xml, which already contains peptideprophet results ... processed altogether 0 results ERROR: output file created, /home/sean/Documents/proteome/interact-interact-20161205_Sample_24A.pep.xml, appears incomplete. Please check the input files for completeness. INFO: Results written to file: /home/sean/Documents/proteome/interact-interact-20161205_Sample_24A.pep.xml command completed in 0 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-interact-20161205_Sample_24A.pep.xml'" command completed in 0 sec No single database specified (by -D option or in .pep.xml file). RefreshParser skipped. running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_24A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN Error: file update failed (did not find closing tag ""), check file interact-interact-20161205_Sample_24A.pep.xml.tmp.ZwZmoM for completeness error: no peptideprophet data written to file interact-interact-20161205_Sample_24A.pep.xml command "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_24A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" exited with non-zero exit code: 256 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_24A.prot.xml.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_24A.prot.xml.pep.xml' 'interact-20161205_Sample_24A.prot.xml.pep.xml' -L'7'" terminate called after throwing an instance of 'boost::exception_detail::clone_impl >' what(): failed opening file: No such file or directory: iostream error Aborted (core dumped) command "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_24A.prot.xml.pep.xml' 'interact-20161205_Sample_24A.prot.xml.pep.xml' -L'7'" exited with non-zero exit code: 34304 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_24.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_24.pep.xml' 'interact-20161205_Sample_24.pep.xml' -L'7'" Skipping file interact-20161205_Sample_24.pep.xml, which already contains peptideprophet results ... processed altogether 0 results ERROR: output file created, /home/sean/Documents/proteome/interact-interact-20161205_Sample_24.pep.xml, appears incomplete. Please check the input files for completeness. INFO: Results written to file: /home/sean/Documents/proteome/interact-interact-20161205_Sample_24.pep.xml command completed in 0 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-interact-20161205_Sample_24.pep.xml'" command completed in 0 sec No single database specified (by -D option or in .pep.xml file). RefreshParser skipped. running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_24.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN Error: file update failed (did not find closing tag ""), check file interact-interact-20161205_Sample_24.pep.xml.tmp.A6DTc7 for completeness error: no peptideprophet data written to file interact-interact-20161205_Sample_24.pep.xml command "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_24.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" exited with non-zero exit code: 256 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_24.prot.xml.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_24.prot.xml.pep.xml' 'interact-20161205_Sample_24.prot.xml.pep.xml' -L'7'" terminate called after throwing an instance of 'boost::exception_detail::clone_impl >' what(): failed opening file: No such file or directory: iostream error Aborted (core dumped) command "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_24.prot.xml.pep.xml' 'interact-20161205_Sample_24.prot.xml.pep.xml' -L'7'" exited with non-zero exit code: 34304 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_27A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_27A.pep.xml' 'interact-20161205_Sample_27A.pep.xml' -L'7'" Skipping file interact-20161205_Sample_27A.pep.xml, which already contains peptideprophet results ... processed altogether 0 results ERROR: output file created, /home/sean/Documents/proteome/interact-interact-20161205_Sample_27A.pep.xml, appears incomplete. Please check the input files for completeness. INFO: Results written to file: /home/sean/Documents/proteome/interact-interact-20161205_Sample_27A.pep.xml command completed in 0 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-interact-20161205_Sample_27A.pep.xml'" command completed in 0 sec No single database specified (by -D option or in .pep.xml file). RefreshParser skipped. running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_27A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN Error: file update failed (did not find closing tag ""), check file interact-interact-20161205_Sample_27A.pep.xml.tmp.Oc235w for completeness error: no peptideprophet data written to file interact-interact-20161205_Sample_27A.pep.xml command "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_27A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" exited with non-zero exit code: 256 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_27A.prot.xml.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_27A.prot.xml.pep.xml' 'interact-20161205_Sample_27A.prot.xml.pep.xml' -L'7'" terminate called after throwing an instance of 'boost::exception_detail::clone_impl >' what(): failed opening file: No such file or directory: iostream error Aborted (core dumped) command "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_27A.prot.xml.pep.xml' 'interact-20161205_Sample_27A.prot.xml.pep.xml' -L'7'" exited with non-zero exit code: 34304 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_27.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_27.pep.xml' 'interact-20161205_Sample_27.pep.xml' -L'7'" Skipping file interact-20161205_Sample_27.pep.xml, which already contains peptideprophet results ... processed altogether 0 results ERROR: output file created, /home/sean/Documents/proteome/interact-interact-20161205_Sample_27.pep.xml, appears incomplete. Please check the input files for completeness. INFO: Results written to file: /home/sean/Documents/proteome/interact-interact-20161205_Sample_27.pep.xml command completed in 0 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-interact-20161205_Sample_27.pep.xml'" command completed in 0 sec No single database specified (by -D option or in .pep.xml file). RefreshParser skipped. running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_27.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN Error: file update failed (did not find closing tag ""), check file interact-interact-20161205_Sample_27.pep.xml.tmp.aQQAuS for completeness error: no peptideprophet data written to file interact-interact-20161205_Sample_27.pep.xml command "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_27.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" exited with non-zero exit code: 256 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_27.prot.xml.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_27.prot.xml.pep.xml' 'interact-20161205_Sample_27.prot.xml.pep.xml' -L'7'" terminate called after throwing an instance of 'boost::exception_detail::clone_impl >' what(): failed opening file: No such file or directory: iostream error Aborted (core dumped) command "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_27.prot.xml.pep.xml' 'interact-20161205_Sample_27.prot.xml.pep.xml' -L'7'" exited with non-zero exit code: 34304 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_28A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_28A.pep.xml' 'interact-20161205_Sample_28A.pep.xml' -L'7'" Skipping file interact-20161205_Sample_28A.pep.xml, which already contains peptideprophet results ... processed altogether 0 results ERROR: output file created, /home/sean/Documents/proteome/interact-interact-20161205_Sample_28A.pep.xml, appears incomplete. Please check the input files for completeness. INFO: Results written to file: /home/sean/Documents/proteome/interact-interact-20161205_Sample_28A.pep.xml command completed in 0 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-interact-20161205_Sample_28A.pep.xml'" command completed in 0 sec No single database specified (by -D option or in .pep.xml file). RefreshParser skipped. running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_28A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN Error: file update failed (did not find closing tag ""), check file interact-interact-20161205_Sample_28A.pep.xml.tmp.GVL1Y8 for completeness error: no peptideprophet data written to file interact-interact-20161205_Sample_28A.pep.xml command "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_28A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" exited with non-zero exit code: 256 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_28A.prot.xml.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_28A.prot.xml.pep.xml' 'interact-20161205_Sample_28A.prot.xml.pep.xml' -L'7'" terminate called after throwing an instance of 'boost::exception_detail::clone_impl >' what(): failed opening file: No such file or directory: iostream error Aborted (core dumped) command "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_28A.prot.xml.pep.xml' 'interact-20161205_Sample_28A.prot.xml.pep.xml' -L'7'" exited with non-zero exit code: 34304 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_28.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_28.pep.xml' 'interact-20161205_Sample_28.pep.xml' -L'7'" Skipping file interact-20161205_Sample_28.pep.xml, which already contains peptideprophet results ... processed altogether 0 results ERROR: output file created, /home/sean/Documents/proteome/interact-interact-20161205_Sample_28.pep.xml, appears incomplete. Please check the input files for completeness. INFO: Results written to file: /home/sean/Documents/proteome/interact-interact-20161205_Sample_28.pep.xml command completed in 0 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-interact-20161205_Sample_28.pep.xml'" command completed in 0 sec No single database specified (by -D option or in .pep.xml file). RefreshParser skipped. running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_28.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN Error: file update failed (did not find closing tag ""), check file interact-interact-20161205_Sample_28.pep.xml.tmp.sgthvu for completeness error: no peptideprophet data written to file interact-interact-20161205_Sample_28.pep.xml command "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_28.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" exited with non-zero exit code: 256 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_28.prot.xml.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_28.prot.xml.pep.xml' 'interact-20161205_Sample_28.prot.xml.pep.xml' -L'7'" terminate called after throwing an instance of 'boost::exception_detail::clone_impl >' what(): failed opening file: No such file or directory: iostream error Aborted (core dumped) command "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_28.prot.xml.pep.xml' 'interact-20161205_Sample_28.prot.xml.pep.xml' -L'7'" exited with non-zero exit code: 34304 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_32A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_32A.pep.xml' 'interact-20161205_Sample_32A.pep.xml' -L'7'" Skipping file interact-20161205_Sample_32A.pep.xml, which already contains peptideprophet results ... processed altogether 0 results ERROR: output file created, /home/sean/Documents/proteome/interact-interact-20161205_Sample_32A.pep.xml, appears incomplete. Please check the input files for completeness. INFO: Results written to file: /home/sean/Documents/proteome/interact-interact-20161205_Sample_32A.pep.xml command completed in 0 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-interact-20161205_Sample_32A.pep.xml'" command completed in 0 sec No single database specified (by -D option or in .pep.xml file). RefreshParser skipped. running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_32A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN Error: file update failed (did not find closing tag ""), check file interact-interact-20161205_Sample_32A.pep.xml.tmp.4d5CdT for completeness error: no peptideprophet data written to file interact-interact-20161205_Sample_32A.pep.xml command "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_32A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" exited with non-zero exit code: 256 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_32A.prot.xml.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_32A.prot.xml.pep.xml' 'interact-20161205_Sample_32A.prot.xml.pep.xml' -L'7'" terminate called after throwing an instance of 'boost::exception_detail::clone_impl >' what(): failed opening file: No such file or directory: iostream error Aborted (core dumped) command "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_32A.prot.xml.pep.xml' 'interact-20161205_Sample_32A.prot.xml.pep.xml' -L'7'" exited with non-zero exit code: 34304 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_32.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_32.pep.xml' 'interact-20161205_Sample_32.pep.xml' -L'7'" Skipping file interact-20161205_Sample_32.pep.xml, which already contains peptideprophet results ... processed altogether 0 results ERROR: output file created, /home/sean/Documents/proteome/interact-interact-20161205_Sample_32.pep.xml, appears incomplete. Please check the input files for completeness. INFO: Results written to file: /home/sean/Documents/proteome/interact-interact-20161205_Sample_32.pep.xml command completed in 0 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-interact-20161205_Sample_32.pep.xml'" command completed in 0 sec No single database specified (by -D option or in .pep.xml file). RefreshParser skipped. running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_32.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN Error: file update failed (did not find closing tag ""), check file interact-interact-20161205_Sample_32.pep.xml.tmp.BLWyBe for completeness error: no peptideprophet data written to file interact-interact-20161205_Sample_32.pep.xml command "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_32.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" exited with non-zero exit code: 256 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_32.prot.xml.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_32.prot.xml.pep.xml' 'interact-20161205_Sample_32.prot.xml.pep.xml' -L'7'" terminate called after throwing an instance of 'boost::exception_detail::clone_impl >' what(): failed opening file: No such file or directory: iostream error Aborted (core dumped) command "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_32.prot.xml.pep.xml' 'interact-20161205_Sample_32.prot.xml.pep.xml' -L'7'" exited with non-zero exit code: 34304 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_35A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_35A.pep.xml' 'interact-20161205_Sample_35A.pep.xml' -L'7'" Skipping file interact-20161205_Sample_35A.pep.xml, which already contains peptideprophet results ... processed altogether 0 results ERROR: output file created, /home/sean/Documents/proteome/interact-interact-20161205_Sample_35A.pep.xml, appears incomplete. Please check the input files for completeness. INFO: Results written to file: /home/sean/Documents/proteome/interact-interact-20161205_Sample_35A.pep.xml command completed in 0 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-interact-20161205_Sample_35A.pep.xml'" command completed in 0 sec No single database specified (by -D option or in .pep.xml file). RefreshParser skipped. running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_35A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN Error: file update failed (did not find closing tag ""), check file interact-interact-20161205_Sample_35A.pep.xml.tmp.1eJRBD for completeness error: no peptideprophet data written to file interact-interact-20161205_Sample_35A.pep.xml command "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_35A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" exited with non-zero exit code: 256 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_35A.prot.xml.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_35A.prot.xml.pep.xml' 'interact-20161205_Sample_35A.prot.xml.pep.xml' -L'7'" terminate called after throwing an instance of 'boost::exception_detail::clone_impl >' what(): failed opening file: No such file or directory: iostream error Aborted (core dumped) command "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_35A.prot.xml.pep.xml' 'interact-20161205_Sample_35A.prot.xml.pep.xml' -L'7'" exited with non-zero exit code: 34304 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_35.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_35.pep.xml' 'interact-20161205_Sample_35.pep.xml' -L'7'" Skipping file interact-20161205_Sample_35.pep.xml, which already contains peptideprophet results ... processed altogether 0 results ERROR: output file created, /home/sean/Documents/proteome/interact-interact-20161205_Sample_35.pep.xml, appears incomplete. Please check the input files for completeness. INFO: Results written to file: /home/sean/Documents/proteome/interact-interact-20161205_Sample_35.pep.xml command completed in 0 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-interact-20161205_Sample_35.pep.xml'" command completed in 0 sec No single database specified (by -D option or in .pep.xml file). RefreshParser skipped. running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_35.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN Error: file update failed (did not find closing tag ""), check file interact-interact-20161205_Sample_35.pep.xml.tmp.86cpsO for completeness error: no peptideprophet data written to file interact-interact-20161205_Sample_35.pep.xml command "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_35.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" exited with non-zero exit code: 256 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_35.prot.xml.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_35.prot.xml.pep.xml' 'interact-20161205_Sample_35.prot.xml.pep.xml' -L'7'" terminate called after throwing an instance of 'boost::exception_detail::clone_impl >' what(): failed opening file: No such file or directory: iostream error Aborted (core dumped) command "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_35.prot.xml.pep.xml' 'interact-20161205_Sample_35.prot.xml.pep.xml' -L'7'" exited with non-zero exit code: 34304 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_36A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_36A.pep.xml' 'interact-20161205_Sample_36A.pep.xml' -L'7'" Skipping file interact-20161205_Sample_36A.pep.xml, which already contains peptideprophet results ... processed altogether 0 results ERROR: output file created, /home/sean/Documents/proteome/interact-interact-20161205_Sample_36A.pep.xml, appears incomplete. Please check the input files for completeness. INFO: Results written to file: /home/sean/Documents/proteome/interact-interact-20161205_Sample_36A.pep.xml command completed in 0 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-interact-20161205_Sample_36A.pep.xml'" command completed in 0 sec No single database specified (by -D option or in .pep.xml file). RefreshParser skipped. running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_36A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN Error: file update failed (did not find closing tag ""), check file interact-interact-20161205_Sample_36A.pep.xml.tmp.jSbydd for completeness error: no peptideprophet data written to file interact-interact-20161205_Sample_36A.pep.xml command "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_36A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" exited with non-zero exit code: 256 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_36A.prot.xml.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_36A.prot.xml.pep.xml' 'interact-20161205_Sample_36A.prot.xml.pep.xml' -L'7'" terminate called after throwing an instance of 'boost::exception_detail::clone_impl >' what(): failed opening file: No such file or directory: iostream error Aborted (core dumped) command "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_36A.prot.xml.pep.xml' 'interact-20161205_Sample_36A.prot.xml.pep.xml' -L'7'" exited with non-zero exit code: 34304 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_36.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_36.pep.xml' 'interact-20161205_Sample_36.pep.xml' -L'7'" Skipping file interact-20161205_Sample_36.pep.xml, which already contains peptideprophet results ... processed altogether 0 results ERROR: output file created, /home/sean/Documents/proteome/interact-interact-20161205_Sample_36.pep.xml, appears incomplete. Please check the input files for completeness. INFO: Results written to file: /home/sean/Documents/proteome/interact-interact-20161205_Sample_36.pep.xml command completed in 0 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-interact-20161205_Sample_36.pep.xml'" command completed in 0 sec No single database specified (by -D option or in .pep.xml file). RefreshParser skipped. running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_36.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN Error: file update failed (did not find closing tag ""), check file interact-interact-20161205_Sample_36.pep.xml.tmp.lRDlVz for completeness error: no peptideprophet data written to file interact-interact-20161205_Sample_36.pep.xml command "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_36.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" exited with non-zero exit code: 256 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_36.prot.xml.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_36.prot.xml.pep.xml' 'interact-20161205_Sample_36.prot.xml.pep.xml' -L'7'" terminate called after throwing an instance of 'boost::exception_detail::clone_impl >' what(): failed opening file: No such file or directory: iostream error Aborted (core dumped) command "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_36.prot.xml.pep.xml' 'interact-20161205_Sample_36.prot.xml.pep.xml' -L'7'" exited with non-zero exit code: 34304 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_3A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_3A.pep.xml' 'interact-20161205_Sample_3A.pep.xml' -L'7'" Skipping file interact-20161205_Sample_3A.pep.xml, which already contains peptideprophet results ... processed altogether 0 results ERROR: output file created, /home/sean/Documents/proteome/interact-interact-20161205_Sample_3A.pep.xml, appears incomplete. Please check the input files for completeness. INFO: Results written to file: /home/sean/Documents/proteome/interact-interact-20161205_Sample_3A.pep.xml command completed in 0 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-interact-20161205_Sample_3A.pep.xml'" command completed in 0 sec No single database specified (by -D option or in .pep.xml file). RefreshParser skipped. running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_3A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN Error: file update failed (did not find closing tag ""), check file interact-interact-20161205_Sample_3A.pep.xml.tmp.GG6woU for completeness error: no peptideprophet data written to file interact-interact-20161205_Sample_3A.pep.xml command "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_3A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" exited with non-zero exit code: 256 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_3A.prot.xml.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_3A.prot.xml.pep.xml' 'interact-20161205_Sample_3A.prot.xml.pep.xml' -L'7'" terminate called after throwing an instance of 'boost::exception_detail::clone_impl >' what(): failed opening file: No such file or directory: iostream error Aborted (core dumped) command "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_3A.prot.xml.pep.xml' 'interact-20161205_Sample_3A.prot.xml.pep.xml' -L'7'" exited with non-zero exit code: 34304 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_3.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_3.pep.xml' 'interact-20161205_Sample_3.pep.xml' -L'7'" Skipping file interact-20161205_Sample_3.pep.xml, which already contains peptideprophet results ... processed altogether 0 results ERROR: output file created, /home/sean/Documents/proteome/interact-interact-20161205_Sample_3.pep.xml, appears incomplete. Please check the input files for completeness. INFO: Results written to file: /home/sean/Documents/proteome/interact-interact-20161205_Sample_3.pep.xml command completed in 0 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-interact-20161205_Sample_3.pep.xml'" command completed in 0 sec No single database specified (by -D option or in .pep.xml file). RefreshParser skipped. running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_3.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN Error: file update failed (did not find closing tag ""), check file interact-interact-20161205_Sample_3.pep.xml.tmp.O1YkIg for completeness error: no peptideprophet data written to file interact-interact-20161205_Sample_3.pep.xml command "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_3.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" exited with non-zero exit code: 256 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_3.prot.xml.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_3.prot.xml.pep.xml' 'interact-20161205_Sample_3.prot.xml.pep.xml' -L'7'" terminate called after throwing an instance of 'boost::exception_detail::clone_impl >' what(): failed opening file: No such file or directory: iostream error Aborted (core dumped) command "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_3.prot.xml.pep.xml' 'interact-20161205_Sample_3.prot.xml.pep.xml' -L'7'" exited with non-zero exit code: 34304 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_40A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_40A.pep.xml' 'interact-20161205_Sample_40A.pep.xml' -L'7'" Skipping file interact-20161205_Sample_40A.pep.xml, which already contains peptideprophet results ... processed altogether 0 results ERROR: output file created, /home/sean/Documents/proteome/interact-interact-20161205_Sample_40A.pep.xml, appears incomplete. Please check the input files for completeness. INFO: Results written to file: /home/sean/Documents/proteome/interact-interact-20161205_Sample_40A.pep.xml command completed in 0 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-interact-20161205_Sample_40A.pep.xml'" command completed in 0 sec No single database specified (by -D option or in .pep.xml file). RefreshParser skipped. running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_40A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN Error: file update failed (did not find closing tag ""), check file interact-interact-20161205_Sample_40A.pep.xml.tmp.rBN8YF for completeness error: no peptideprophet data written to file interact-interact-20161205_Sample_40A.pep.xml command "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_40A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" exited with non-zero exit code: 256 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_40A.prot.xml.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_40A.prot.xml.pep.xml' 'interact-20161205_Sample_40A.prot.xml.pep.xml' -L'7'" terminate called after throwing an instance of 'boost::exception_detail::clone_impl >' what(): failed opening file: No such file or directory: iostream error Aborted (core dumped) command "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_40A.prot.xml.pep.xml' 'interact-20161205_Sample_40A.prot.xml.pep.xml' -L'7'" exited with non-zero exit code: 34304 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_40.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_40.pep.xml' 'interact-20161205_Sample_40.pep.xml' -L'7'" Skipping file interact-20161205_Sample_40.pep.xml, which already contains peptideprophet results ... processed altogether 0 results ERROR: output file created, /home/sean/Documents/proteome/interact-interact-20161205_Sample_40.pep.xml, appears incomplete. Please check the input files for completeness. INFO: Results written to file: /home/sean/Documents/proteome/interact-interact-20161205_Sample_40.pep.xml command completed in 0 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-interact-20161205_Sample_40.pep.xml'" command completed in 0 sec No single database specified (by -D option or in .pep.xml file). RefreshParser skipped. running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_40.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN Error: file update failed (did not find closing tag ""), check file interact-interact-20161205_Sample_40.pep.xml.tmp.1lHGCQ for completeness error: no peptideprophet data written to file interact-interact-20161205_Sample_40.pep.xml command "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_40.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" exited with non-zero exit code: 256 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_40.prot.xml.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_40.prot.xml.pep.xml' 'interact-20161205_Sample_40.prot.xml.pep.xml' -L'7'" terminate called after throwing an instance of 'boost::exception_detail::clone_impl >' what(): failed opening file: No such file or directory: iostream error Aborted (core dumped) command "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_40.prot.xml.pep.xml' 'interact-20161205_Sample_40.prot.xml.pep.xml' -L'7'" exited with non-zero exit code: 34304 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_43A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_43A.pep.xml' 'interact-20161205_Sample_43A.pep.xml' -L'7'" Skipping file interact-20161205_Sample_43A.pep.xml, which already contains peptideprophet results ... processed altogether 0 results ERROR: output file created, /home/sean/Documents/proteome/interact-interact-20161205_Sample_43A.pep.xml, appears incomplete. Please check the input files for completeness. INFO: Results written to file: /home/sean/Documents/proteome/interact-interact-20161205_Sample_43A.pep.xml command completed in 0 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-interact-20161205_Sample_43A.pep.xml'" command completed in 0 sec No single database specified (by -D option or in .pep.xml file). RefreshParser skipped. running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_43A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN Error: file update failed (did not find closing tag ""), check file interact-interact-20161205_Sample_43A.pep.xml.tmp.1hmDif for completeness error: no peptideprophet data written to file interact-interact-20161205_Sample_43A.pep.xml command "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_43A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" exited with non-zero exit code: 256 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_43A.prot.xml.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_43A.prot.xml.pep.xml' 'interact-20161205_Sample_43A.prot.xml.pep.xml' -L'7'" terminate called after throwing an instance of 'boost::exception_detail::clone_impl >' what(): failed opening file: No such file or directory: iostream error Aborted (core dumped) command "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_43A.prot.xml.pep.xml' 'interact-20161205_Sample_43A.prot.xml.pep.xml' -L'7'" exited with non-zero exit code: 34304 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_43.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_43.pep.xml' 'interact-20161205_Sample_43.pep.xml' -L'7'" Skipping file interact-20161205_Sample_43.pep.xml, which already contains peptideprophet results ... processed altogether 0 results ERROR: output file created, /home/sean/Documents/proteome/interact-interact-20161205_Sample_43.pep.xml, appears incomplete. Please check the input files for completeness. INFO: Results written to file: /home/sean/Documents/proteome/interact-interact-20161205_Sample_43.pep.xml command completed in 0 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-interact-20161205_Sample_43.pep.xml'" command completed in 0 sec No single database specified (by -D option or in .pep.xml file). RefreshParser skipped. running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_43.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN Error: file update failed (did not find closing tag ""), check file interact-interact-20161205_Sample_43.pep.xml.tmp.VWHX8B for completeness error: no peptideprophet data written to file interact-interact-20161205_Sample_43.pep.xml command "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_43.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" exited with non-zero exit code: 256 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_43.prot.xml.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_43.prot.xml.pep.xml' 'interact-20161205_Sample_43.prot.xml.pep.xml' -L'7'" terminate called after throwing an instance of 'boost::exception_detail::clone_impl >' what(): failed opening file: No such file or directory: iostream error Aborted (core dumped) command "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_43.prot.xml.pep.xml' 'interact-20161205_Sample_43.prot.xml.pep.xml' -L'7'" exited with non-zero exit code: 34304 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_44A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_44A.pep.xml' 'interact-20161205_Sample_44A.pep.xml' -L'7'" Skipping file interact-20161205_Sample_44A.pep.xml, which already contains peptideprophet results ... processed altogether 0 results ERROR: output file created, /home/sean/Documents/proteome/interact-interact-20161205_Sample_44A.pep.xml, appears incomplete. Please check the input files for completeness. INFO: Results written to file: /home/sean/Documents/proteome/interact-interact-20161205_Sample_44A.pep.xml command completed in 0 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-interact-20161205_Sample_44A.pep.xml'" command completed in 0 sec No single database specified (by -D option or in .pep.xml file). RefreshParser skipped. running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_44A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN Error: file update failed (did not find closing tag ""), check file interact-interact-20161205_Sample_44A.pep.xml.tmp.KR87mW for completeness error: no peptideprophet data written to file interact-interact-20161205_Sample_44A.pep.xml command "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_44A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" exited with non-zero exit code: 256 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_44A.prot.xml.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_44A.prot.xml.pep.xml' 'interact-20161205_Sample_44A.prot.xml.pep.xml' -L'7'" terminate called after throwing an instance of 'boost::exception_detail::clone_impl >' what(): failed opening file: No such file or directory: iostream error Aborted (core dumped) command "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_44A.prot.xml.pep.xml' 'interact-20161205_Sample_44A.prot.xml.pep.xml' -L'7'" exited with non-zero exit code: 34304 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_44.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_44.pep.xml' 'interact-20161205_Sample_44.pep.xml' -L'7'" Skipping file interact-20161205_Sample_44.pep.xml, which already contains peptideprophet results ... processed altogether 0 results ERROR: output file created, /home/sean/Documents/proteome/interact-interact-20161205_Sample_44.pep.xml, appears incomplete. Please check the input files for completeness. INFO: Results written to file: /home/sean/Documents/proteome/interact-interact-20161205_Sample_44.pep.xml command completed in 0 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-interact-20161205_Sample_44.pep.xml'" command completed in 0 sec No single database specified (by -D option or in .pep.xml file). RefreshParser skipped. running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_44.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN Error: file update failed (did not find closing tag ""), check file interact-interact-20161205_Sample_44.pep.xml.tmp.UIPzMi for completeness error: no peptideprophet data written to file interact-interact-20161205_Sample_44.pep.xml command "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_44.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" exited with non-zero exit code: 256 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_44.prot.xml.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_44.prot.xml.pep.xml' 'interact-20161205_Sample_44.prot.xml.pep.xml' -L'7'" terminate called after throwing an instance of 'boost::exception_detail::clone_impl >' what(): failed opening file: No such file or directory: iostream error Aborted (core dumped) command "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_44.prot.xml.pep.xml' 'interact-20161205_Sample_44.prot.xml.pep.xml' -L'7'" exited with non-zero exit code: 34304 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_48A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_48A.pep.xml' 'interact-20161205_Sample_48A.pep.xml' -L'7'" Skipping file interact-20161205_Sample_48A.pep.xml, which already contains peptideprophet results ... processed altogether 0 results ERROR: output file created, /home/sean/Documents/proteome/interact-interact-20161205_Sample_48A.pep.xml, appears incomplete. Please check the input files for completeness. INFO: Results written to file: /home/sean/Documents/proteome/interact-interact-20161205_Sample_48A.pep.xml command completed in 0 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-interact-20161205_Sample_48A.pep.xml'" command completed in 0 sec No single database specified (by -D option or in .pep.xml file). RefreshParser skipped. running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_48A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN Error: file update failed (did not find closing tag ""), check file interact-interact-20161205_Sample_48A.pep.xml.tmp.V0itCI for completeness error: no peptideprophet data written to file interact-interact-20161205_Sample_48A.pep.xml command "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_48A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" exited with non-zero exit code: 256 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_48A.prot.xml.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_48A.prot.xml.pep.xml' 'interact-20161205_Sample_48A.prot.xml.pep.xml' -L'7'" terminate called after throwing an instance of 'boost::exception_detail::clone_impl >' what(): failed opening file: No such file or directory: iostream error Aborted (core dumped) command "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_48A.prot.xml.pep.xml' 'interact-20161205_Sample_48A.prot.xml.pep.xml' -L'7'" exited with non-zero exit code: 34304 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_48.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_48.pep.xml' 'interact-20161205_Sample_48.pep.xml' -L'7'" Skipping file interact-20161205_Sample_48.pep.xml, which already contains peptideprophet results ... processed altogether 0 results ERROR: output file created, /home/sean/Documents/proteome/interact-interact-20161205_Sample_48.pep.xml, appears incomplete. Please check the input files for completeness. INFO: Results written to file: /home/sean/Documents/proteome/interact-interact-20161205_Sample_48.pep.xml command completed in 0 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-interact-20161205_Sample_48.pep.xml'" command completed in 0 sec No single database specified (by -D option or in .pep.xml file). RefreshParser skipped. running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_48.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN Error: file update failed (did not find closing tag ""), check file interact-interact-20161205_Sample_48.pep.xml.tmp.dJeYPV for completeness error: no peptideprophet data written to file interact-interact-20161205_Sample_48.pep.xml command "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_48.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" exited with non-zero exit code: 256 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_48.prot.xml.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_48.prot.xml.pep.xml' 'interact-20161205_Sample_48.prot.xml.pep.xml' -L'7'" terminate called after throwing an instance of 'boost::exception_detail::clone_impl >' what(): failed opening file: No such file or directory: iostream error Aborted (core dumped) command "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_48.prot.xml.pep.xml' 'interact-20161205_Sample_48.prot.xml.pep.xml' -L'7'" exited with non-zero exit code: 34304 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_4A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_4A.pep.xml' 'interact-20161205_Sample_4A.pep.xml' -L'7'" Skipping file interact-20161205_Sample_4A.pep.xml, which already contains peptideprophet results ... processed altogether 0 results ERROR: output file created, /home/sean/Documents/proteome/interact-interact-20161205_Sample_4A.pep.xml, appears incomplete. Please check the input files for completeness. INFO: Results written to file: /home/sean/Documents/proteome/interact-interact-20161205_Sample_4A.pep.xml command completed in 0 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-interact-20161205_Sample_4A.pep.xml'" command completed in 0 sec No single database specified (by -D option or in .pep.xml file). RefreshParser skipped. running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_4A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN Error: file update failed (did not find closing tag ""), check file interact-interact-20161205_Sample_4A.pep.xml.tmp.0RzZsi for completeness error: no peptideprophet data written to file interact-interact-20161205_Sample_4A.pep.xml command "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_4A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" exited with non-zero exit code: 256 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_4A.prot.xml.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_4A.prot.xml.pep.xml' 'interact-20161205_Sample_4A.prot.xml.pep.xml' -L'7'" terminate called after throwing an instance of 'boost::exception_detail::clone_impl >' what(): failed opening file: No such file or directory: iostream error Aborted (core dumped) command "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_4A.prot.xml.pep.xml' 'interact-20161205_Sample_4A.prot.xml.pep.xml' -L'7'" exited with non-zero exit code: 34304 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_4.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_4.pep.xml' 'interact-20161205_Sample_4.pep.xml' -L'7'" Skipping file interact-20161205_Sample_4.pep.xml, which already contains peptideprophet results ... processed altogether 0 results ERROR: output file created, /home/sean/Documents/proteome/interact-interact-20161205_Sample_4.pep.xml, appears incomplete. Please check the input files for completeness. INFO: Results written to file: /home/sean/Documents/proteome/interact-interact-20161205_Sample_4.pep.xml command completed in 0 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-interact-20161205_Sample_4.pep.xml'" command completed in 0 sec No single database specified (by -D option or in .pep.xml file). RefreshParser skipped. running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_4.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN Error: file update failed (did not find closing tag ""), check file interact-interact-20161205_Sample_4.pep.xml.tmp.TJPXKC for completeness error: no peptideprophet data written to file interact-interact-20161205_Sample_4.pep.xml command "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_4.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" exited with non-zero exit code: 256 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_4.prot.xml.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_4.prot.xml.pep.xml' 'interact-20161205_Sample_4.prot.xml.pep.xml' -L'7'" terminate called after throwing an instance of 'boost::exception_detail::clone_impl >' what(): failed opening file: No such file or directory: iostream error Aborted (core dumped) command "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_4.prot.xml.pep.xml' 'interact-20161205_Sample_4.prot.xml.pep.xml' -L'7'" exited with non-zero exit code: 34304 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_51A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_51A.pep.xml' 'interact-20161205_Sample_51A.pep.xml' -L'7'" Skipping file interact-20161205_Sample_51A.pep.xml, which already contains peptideprophet results ... processed altogether 0 results ERROR: output file created, /home/sean/Documents/proteome/interact-interact-20161205_Sample_51A.pep.xml, appears incomplete. Please check the input files for completeness. INFO: Results written to file: /home/sean/Documents/proteome/interact-interact-20161205_Sample_51A.pep.xml command completed in 0 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-interact-20161205_Sample_51A.pep.xml'" command completed in 0 sec No single database specified (by -D option or in .pep.xml file). RefreshParser skipped. running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_51A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN Error: file update failed (did not find closing tag ""), check file interact-interact-20161205_Sample_51A.pep.xml.tmp.bOJadZ for completeness error: no peptideprophet data written to file interact-interact-20161205_Sample_51A.pep.xml command "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_51A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" exited with non-zero exit code: 256 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_51A.prot.xml.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_51A.prot.xml.pep.xml' 'interact-20161205_Sample_51A.prot.xml.pep.xml' -L'7'" terminate called after throwing an instance of 'boost::exception_detail::clone_impl >' what(): failed opening file: No such file or directory: iostream error Aborted (core dumped) command "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_51A.prot.xml.pep.xml' 'interact-20161205_Sample_51A.prot.xml.pep.xml' -L'7'" exited with non-zero exit code: 34304 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_51.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_51.pep.xml' 'interact-20161205_Sample_51.pep.xml' -L'7'" Skipping file interact-20161205_Sample_51.pep.xml, which already contains peptideprophet results ... processed altogether 0 results ERROR: output file created, /home/sean/Documents/proteome/interact-interact-20161205_Sample_51.pep.xml, appears incomplete. Please check the input files for completeness. INFO: Results written to file: /home/sean/Documents/proteome/interact-interact-20161205_Sample_51.pep.xml command completed in 0 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-interact-20161205_Sample_51.pep.xml'" command completed in 0 sec No single database specified (by -D option or in .pep.xml file). RefreshParser skipped. running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_51.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN Error: file update failed (did not find closing tag ""), check file interact-interact-20161205_Sample_51.pep.xml.tmp.eSqgko for completeness error: no peptideprophet data written to file interact-interact-20161205_Sample_51.pep.xml command "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_51.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" exited with non-zero exit code: 256 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_51.prot.xml.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_51.prot.xml.pep.xml' 'interact-20161205_Sample_51.prot.xml.pep.xml' -L'7'" terminate called after throwing an instance of 'boost::exception_detail::clone_impl >' what(): failed opening file: No such file or directory: iostream error Aborted (core dumped) command "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_51.prot.xml.pep.xml' 'interact-20161205_Sample_51.prot.xml.pep.xml' -L'7'" exited with non-zero exit code: 34304 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_52A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_52A.pep.xml' 'interact-20161205_Sample_52A.pep.xml' -L'7'" Skipping file interact-20161205_Sample_52A.pep.xml, which already contains peptideprophet results ... processed altogether 0 results ERROR: output file created, /home/sean/Documents/proteome/interact-interact-20161205_Sample_52A.pep.xml, appears incomplete. Please check the input files for completeness. INFO: Results written to file: /home/sean/Documents/proteome/interact-interact-20161205_Sample_52A.pep.xml command completed in 0 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-interact-20161205_Sample_52A.pep.xml'" command completed in 0 sec No single database specified (by -D option or in .pep.xml file). RefreshParser skipped. running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_52A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN Error: file update failed (did not find closing tag ""), check file interact-interact-20161205_Sample_52A.pep.xml.tmp.tpQVWK for completeness error: no peptideprophet data written to file interact-interact-20161205_Sample_52A.pep.xml command "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_52A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" exited with non-zero exit code: 256 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_52A.prot.xml.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_52A.prot.xml.pep.xml' 'interact-20161205_Sample_52A.prot.xml.pep.xml' -L'7'" terminate called after throwing an instance of 'boost::exception_detail::clone_impl >' what(): failed opening file: No such file or directory: iostream error Aborted (core dumped) command "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_52A.prot.xml.pep.xml' 'interact-20161205_Sample_52A.prot.xml.pep.xml' -L'7'" exited with non-zero exit code: 34304 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_52.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_52.pep.xml' 'interact-20161205_Sample_52.pep.xml' -L'7'" Skipping file interact-20161205_Sample_52.pep.xml, which already contains peptideprophet results ... processed altogether 0 results ERROR: output file created, /home/sean/Documents/proteome/interact-interact-20161205_Sample_52.pep.xml, appears incomplete. Please check the input files for completeness. INFO: Results written to file: /home/sean/Documents/proteome/interact-interact-20161205_Sample_52.pep.xml command completed in 0 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-interact-20161205_Sample_52.pep.xml'" command completed in 0 sec No single database specified (by -D option or in .pep.xml file). RefreshParser skipped. running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_52.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN Error: file update failed (did not find closing tag ""), check file interact-interact-20161205_Sample_52.pep.xml.tmp.USJu2X for completeness error: no peptideprophet data written to file interact-interact-20161205_Sample_52.pep.xml command "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_52.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" exited with non-zero exit code: 256 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_52.prot.xml.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_52.prot.xml.pep.xml' 'interact-20161205_Sample_52.prot.xml.pep.xml' -L'7'" terminate called after throwing an instance of 'boost::exception_detail::clone_impl >' what(): failed opening file: No such file or directory: iostream error Aborted (core dumped) command "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_52.prot.xml.pep.xml' 'interact-20161205_Sample_52.prot.xml.pep.xml' -L'7'" exited with non-zero exit code: 34304 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_56A.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_56A.pep.xml' 'interact-20161205_Sample_56A.pep.xml' -L'7'" Skipping file interact-20161205_Sample_56A.pep.xml, which already contains peptideprophet results ... processed altogether 0 results ERROR: output file created, /home/sean/Documents/proteome/interact-interact-20161205_Sample_56A.pep.xml, appears incomplete. Please check the input files for completeness. INFO: Results written to file: /home/sean/Documents/proteome/interact-interact-20161205_Sample_56A.pep.xml command completed in 0 sec running: "/usr/tpp_install/tpp/bin/DatabaseParser 'interact-interact-20161205_Sample_56A.pep.xml'" command completed in 0 sec No single database specified (by -D option or in .pep.xml file). RefreshParser skipped. running: "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_56A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" using Accurate Mass Bins Using Decoy Label "DECOY_". MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN Error: file update failed (did not find closing tag ""), check file interact-interact-20161205_Sample_56A.pep.xml.tmp.4oscFj for completeness error: no peptideprophet data written to file interact-interact-20161205_Sample_56A.pep.xml command "/usr/tpp_install/tpp/bin/PeptideProphetParser 'interact-interact-20161205_Sample_56A.pep.xml' DECOY=DECOY_ MINPROB=0.9 ACCMASS" exited with non-zero exit code: 256 QUIT - the job is incomplete /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64)) naming output file interact-interact-20161205_Sample_56A.prot.xml.pep.xml running: "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_56A.prot.xml.pep.xml' 'interact-20161205_Sample_56A.prot.xml.pep.xml' -L'7'" terminate called after throwing an instance of 'boost::exception_detail::clone_impl >' what(): failed opening file: No such file or directory: iostream error Aborted (core dumped) command "/usr/tpp_install/tpp/bin/InteractParser 'interact-interact-20161205_Sample_56A.prot.xml.pep.xml' 'interact-20161205_Sample_56A.prot.xml.pep.xml' -L'7'" exited with non-zero exit code: 34304 QUIT - the job is incomplete