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/steven/bioinfo/021217/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 Reading in /home/steven/bioinfo/021217/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 Reading in /home/steven/bioinfo/021217/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 Reading in /home/steven/bioinfo/021217/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 Reading in /home/steven/bioinfo/021217/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 Reading in /home/steven/bioinfo/021217/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 Reading in /home/steven/bioinfo/021217/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 Reading in /home/steven/bioinfo/021217/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 Reading in /home/steven/bioinfo/021217/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 Reading in /home/steven/bioinfo/021217/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 Reading in /home/steven/bioinfo/021217/interact-20161205_Sample_20A.pep.xml... did not find any PeptideProphet results in input data! Did you forget to run PeptideProphet? ...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /home/steven/bioinfo/021217/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 Reading in /home/steven/bioinfo/021217/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 Reading in /home/steven/bioinfo/021217/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 Reading in /home/steven/bioinfo/021217/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 Reading in /home/steven/bioinfo/021217/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 Reading in /home/steven/bioinfo/021217/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 Reading in /home/steven/bioinfo/021217/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 Reading in /home/steven/bioinfo/021217/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 Reading in /home/steven/bioinfo/021217/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 Reading in /home/steven/bioinfo/021217/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 Reading in /home/steven/bioinfo/021217/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 Reading in /home/steven/bioinfo/021217/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 Reading in /home/steven/bioinfo/021217/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 Reading in /home/steven/bioinfo/021217/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 Reading in /home/steven/bioinfo/021217/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 Reading in /home/steven/bioinfo/021217/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 Reading in /home/steven/bioinfo/021217/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 Reading in /home/steven/bioinfo/021217/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 Reading in /home/steven/bioinfo/021217/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 Reading in /home/steven/bioinfo/021217/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 Reading in /home/steven/bioinfo/021217/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 Reading in /home/steven/bioinfo/021217/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 Reading in /home/steven/bioinfo/021217/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 Reading in /home/steven/bioinfo/021217/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 Reading in /home/steven/bioinfo/021217/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 Reading in /home/steven/bioinfo/021217/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 Reading in /home/steven/bioinfo/021217/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 Reading in /home/steven/bioinfo/021217/interact-20161205_Sample_52A.pep.xml... ...read in 0 1+, 19013 2+, 11285 3+, 2012 4+, 230 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /home/steven/bioinfo/021217/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 Reading in /home/steven/bioinfo/021217/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 Reading in /home/steven/bioinfo/021217/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 Reading in /home/steven/bioinfo/021217/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 Reading in /home/steven/bioinfo/021217/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 88386 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 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Total: 40751 Computing degenerate peptides for 20639 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 22734 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 22734 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 22734 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 22734 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 22734 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 22734 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 22734 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 22734 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 17272 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 22734 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=2.63626e-05, db_size=40397625 Finished. Results written to: /home/steven/bioinfo/021217/interact-COMBINED.prot.xml