Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): /Volumes/Serine/wd/18-04-27/zr2096_10_s1_R1_val_1.fq.gz /Volumes/Serine/wd/18-04-27/zr2096_10_s1_R2_val_2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Current working directory is: /Volumes/Serine/wd/18-05-10 Now reading in and storing sequence information of the genome specified in: /Volumes/Serine/wd/18-03-15/genome/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /Volumes/Serine/wd/18-04-27/zr2096_10_s1_R1_val_1.fq.gz and /Volumes/Serine/wd/18-04-27/zr2096_10_s1_R2_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file zr2096_10_s1_R1_val_1.fq.gz to zr2096_10_s1_R1_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_10_s1_R1_val_1.fq.gz to zr2096_10_s1_R1_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_10_s1_R1_val_1.fq.gz (17448883 sequences in total) Writing a C -> T converted version of the input file zr2096_10_s1_R2_val_2.fq.gz to zr2096_10_s1_R2_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_10_s1_R2_val_2.fq.gz to zr2096_10_s1_R2_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_10_s1_R2_val_2.fq.gz (17448883 sequences in total) Input files are zr2096_10_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_10_s1_R1_val_1.fq.gz_G_to_A.fastq and zr2096_10_s1_R2_val_2.fq.gz_C_to_T.fastq and zr2096_10_s1_R2_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /Volumes/Serine/wd/18-03-15/genome/ with the specified options: -q --score-min L,0,-0.9 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr2096_10_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_10_s1_R2_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.9 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:2:1101:1232:2155_1:N:0:GATCAG/1 77 * 0 0 * * 0 0 ATTGTATTAATTATAAAAAATATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNATTTATTATTAAAAATATTAAATA FFFFFFFFFBFFFFFFFFFFFFF#################################<>> Writing bisulfite mapping results to zr2096_10_s1_R1_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /Volumes/Serine/wd/18-04-27/zr2096_10_s1_R1_val_1.fq.gz and /Volumes/Serine/wd/18-04-27/zr2096_10_s1_R2_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far 174417417484888488833 re883 re reaadsdads; ;s;o f of tothesef thehese::s e: 17441744888388 ( 1083 (170.00%) 100we.4488830 (re0100 %) wpaired; of theerse:.0 0 e12%) were pa p90aired;i347 re6of d(; of t these: hese: 1291 113045474031 ( (17448883 reads; of these: 17448883 (100.00%) were paired; of these: 13037214 (74.777347.72.95%) 6%4ali.%0) )a alignegnd edconl ccioogrnedd0%n) ancordatnat lilycgolnnye 0c0d otimes rctdioancord ntlymeans tly 0 0 t 18it5m3i19908e (mes 10s.63% 4 2) 419 (11al19109.i1gn058ed c06onc%467o3 )( al1ri0.89gnedd% 5 ()ca al1niot0glnc.yn96ed co oncore%dxar)ntldan aly eixaagctlntctly y1l y t ei1d m timeexactl e c yo 26nco1 2368r5t659imed 76 (79 antl1 y (5 .256e11%14.x2) a433 lig6an6ce(t14.ly%6 91d c %o) alincordantly ) a>tl1 tiiiggmesmnee n26de d 263con 3.cc0ordan0%t572lo ( 15.yn0o >1vcer tim9oear%)dants alll lyalignign >ment r25.1 t2aiet4%mesd over 25all ac.28lig% eo novncomerent ratedarall al igntly nm>1 tient mes 26.05% overratalle alignment rate Processed 17448883 sequences in total Successfully deleted the temporary files zr2096_10_s1_R1_val_1.fq.gz_C_to_T.fastq, zr2096_10_s1_R1_val_1.fq.gz_G_to_A.fastq, zr2096_10_s1_R2_val_2.fq.gz_C_to_T.fastq and zr2096_10_s1_R2_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 17448883 Final Cytosine Methylation Report ================================= Total number of C's analysed: 217110446 Total methylated C's in CpG context: 22140526 Total methylated C's in CHG context: 1124770 Total methylated C's in CHH context: 4146319 Total methylated C's in Unknown context: 278829 Total unmethylated C's in CpG context: 8743035 Total unmethylated C's in CHG context: 47970312 Total unmethylated C's in CHH context: 132985484 Total unmethylated C's in Unknown context: 1409409 C methylated in CpG context: 71.7% C methylated in CHG context: 2.3% C methylated in CHH context: 3.0% C methylated in unknown context (CN or CHN): 16.5% Bismark completed in 0d 2h 27m 19s ==================== Bismark run complete ==================== Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_10_s1_R1_val_1_bismark_bt2_PE_report.html_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_10_s1_R1_val_1_bismark_bt2_PE_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_10_s1_R1_val_1_bismark_bt2_pe.bam_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): /Volumes/Serine/wd/18-04-27/zr2096_1_s1_R1_val_1.fq.gz /Volumes/Serine/wd/18-04-27/zr2096_1_s1_R2_val_2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Current working directory is: /Volumes/Serine/wd/18-05-10 Now reading in and storing sequence information of the genome specified in: /Volumes/Serine/wd/18-03-15/genome/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /Volumes/Serine/wd/18-04-27/zr2096_1_s1_R1_val_1.fq.gz and /Volumes/Serine/wd/18-04-27/zr2096_1_s1_R2_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file zr2096_1_s1_R1_val_1.fq.gz to zr2096_1_s1_R1_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_1_s1_R1_val_1.fq.gz to zr2096_1_s1_R1_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_1_s1_R1_val_1.fq.gz (28603346 sequences in total) Writing a C -> T converted version of the input file zr2096_1_s1_R2_val_2.fq.gz to zr2096_1_s1_R2_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_1_s1_R2_val_2.fq.gz to zr2096_1_s1_R2_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_1_s1_R2_val_2.fq.gz (28603346 sequences in total) Input files are zr2096_1_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_1_s1_R1_val_1.fq.gz_G_to_A.fastq and zr2096_1_s1_R2_val_2.fq.gz_C_to_T.fastq and zr2096_1_s1_R2_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /Volumes/Serine/wd/18-03-15/genome/ with the specified options: -q --score-min L,0,-0.9 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr2096_1_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_1_s1_R2_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.9 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1249:2156_1:N:0:CGATGT/1 99 NC_035780.1_CT_converted 54035224 6 27M4I48M = 54035615 471 GATTATTTGTTGTTTGTTGTTTGTTTGNNNNTNNNTNNGTTTGTTTGTTTGTTTGTTTGTTTGTAAATTTTTTATATTT FFFFFFFFFFFFFFFFFFFFFFFFFFF####<###<##<<>> Writing bisulfite mapping results to zr2096_1_s1_R1_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /Volumes/Serine/wd/18-04-27/zr2096_1_s1_R1_val_1.fq.gz and /Volumes/Serine/wd/18-04-27/zr2096_1_s1_R2_val_2.fq.gz Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1104:3705:43673_1:N:0:CGATGT NC_035780.1 1 Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far 2286860334262 read8s60;334680603 or334ea36d4f 6s; oft rereaadshe; ds;so of tf the:eh seese :t 2 hese:8: 60328 34 603 23 46 8620368 (3 (4100.6033466 1 (0100(00.10000.0%.0)000% %%))) we ww wereerr eere pe paiapi rrpairedai; orfed; eof det;dht;eh os e: ese: fo th2 f 5esthe125898e17:se: 8 3 49 8 9 (252511785(6058888.039.07%) align7 7 (1%ed )8 a8(l.cig8028.o%nn)0 e5d%) aclo concordanridanatligned gnedlt coyn c0lcoy rdti0o mntecaiontlmsyr edsa 0 n tt l ime sy11337719 0 t8 i 0794m2 1 e(s3 4.882 ( 30% 71 4.8(131)4.83% )ali% 7)gn 88aale5dl1 ii( ggnedcon4ncorda.end t8l 2cc%)oy ncord aoalincongrndeaed xncactoly tnlyextcl ordantley 1ya ctltxacy 1 imeetly x 1 time actl2 0ty 1 32t2im0e651165 629 ((7.0i7.11m71e%) al 3igne%88d ) c o9 n2a (lign7.1ce3odrd% con20) a4alni5tg2l98ney d conco c(r>7doan1rtly >1.15 dtimaes% tnim) atel s yl i111.9>5g1%.91 ti nomevedse ra lconl cord311% .aloveantlyi >99r1ag ltlnime%m oent rs v1ea1lrall igna.9ate8mligne %m eontvnt rraaterae ltel alignment rate Processed 28603346 sequences in total Successfully deleted the temporary files zr2096_1_s1_R1_val_1.fq.gz_C_to_T.fastq, zr2096_1_s1_R1_val_1.fq.gz_G_to_A.fastq, zr2096_1_s1_R2_val_2.fq.gz_C_to_T.fastq and zr2096_1_s1_R2_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 28603346 Final Cytosine Methylation Report ================================= Total number of C's analysed: 151944296 Total methylated C's in CpG context: 14107636 Total methylated C's in CHG context: 820467 Total methylated C's in CHH context: 5833007 Total methylated C's in Unknown context: 375906 Total unmethylated C's in CpG context: 5366165 Total unmethylated C's in CHG context: 31159480 Total unmethylated C's in CHH context: 94657541 Total unmethylated C's in Unknown context: 1269671 C methylated in CpG context: 72.4% C methylated in CHG context: 2.6% C methylated in CHH context: 5.8% C methylated in unknown context (CN or CHN): 22.8% Bismark completed in 0d 2h 37m 30s ==================== Bismark run complete ==================== Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_1_s1_R1_val_1_bismark_bt2_PE_report.html_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_1_s1_R1_val_1_bismark_bt2_PE_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_1_s1_R1_val_1_bismark_bt2_pe.bam_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): /Volumes/Serine/wd/18-04-27/zr2096_2_s1_R1_val_1.fq.gz /Volumes/Serine/wd/18-04-27/zr2096_2_s1_R2_val_2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Current working directory is: /Volumes/Serine/wd/18-05-10 Now reading in and storing sequence information of the genome specified in: /Volumes/Serine/wd/18-03-15/genome/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /Volumes/Serine/wd/18-04-27/zr2096_2_s1_R1_val_1.fq.gz and /Volumes/Serine/wd/18-04-27/zr2096_2_s1_R2_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file zr2096_2_s1_R1_val_1.fq.gz to zr2096_2_s1_R1_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_2_s1_R1_val_1.fq.gz to zr2096_2_s1_R1_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_2_s1_R1_val_1.fq.gz (30325606 sequences in total) Writing a C -> T converted version of the input file zr2096_2_s1_R2_val_2.fq.gz to zr2096_2_s1_R2_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_2_s1_R2_val_2.fq.gz to zr2096_2_s1_R2_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_2_s1_R2_val_2.fq.gz (30325606 sequences in total) Input files are zr2096_2_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_2_s1_R1_val_1.fq.gz_G_to_A.fastq and zr2096_2_s1_R2_val_2.fq.gz_C_to_T.fastq and zr2096_2_s1_R2_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /Volumes/Serine/wd/18-03-15/genome/ with the specified options: -q --score-min L,0,-0.9 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr2096_2_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_2_s1_R2_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.9 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1148:2157_1:N:0:TGACCA/1 77 * 0 0 * * 0 0 AAATTTATTATTTTAAAAATAAAAATTNNNNTNNNTTTTATTATTTTTTTTAATATTTTTTAATATAATTAAATAATAA FFFFFFFFFFFFFFFFFFFFFFFFFFF####<###<<>> Writing bisulfite mapping results to zr2096_2_s1_R1_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /Volumes/Serine/wd/18-04-27/zr2096_2_s1_R1_val_1.fq.gz and /Volumes/Serine/wd/18-04-27/zr2096_2_s1_R2_val_2.fq.gz Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1101:20975:44723_1:N:0:TGACCA NC_035781.1 1 Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1210:4310:17386_1:N:0:TGACCA NC_035780.1 1 Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1316:4047:74652_1:N:0:TGACCA NC_007175.2 17170 Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far 3303303256060 reads; of these:0325 3263 56200566 r 6r30e0ads; of these:32 6 e5 303256066a 0(reads; o160f these:0.0ds; of thes0%) were paired; of these: 22483139 (74.14%) aligned concordantly 0 times 3179561 (10.48%) aligned concordant e: 3 l0 y (30325601006 e 3.x(256060 a1(0%10) w000.0e.cr00e%t 0)ly w% p)e1a wirre tree e ipdpmea ;ired; of aired; of these:4o6t6 2f h9t 0he6s ( 12ee: 52 5.38se : 2% 729724 () 7 5 8242487.4a16li%gned conc)o 70a70r81l i((7474.4d.15%g) al8igneda%n concordatly >1 t) alignineemnes d25.8t col6dy n%c ovecoral0 toli ancordamrlesdiantlgnymn tent ly r031660 a2t te itimes0 m e s 8 31(21313343341 (08.44140.3%3) a%ligned (c1)0o .a2nlcor9%)dant alyili exggnedned coactly 1 timnce o cor n4dcantoly6 red7xantly exa2228a cc(t1t5.41%) laligney ly 1 tim1 timee d46 1 c2449o 461n(cordantly >1 t7i041 1(m1e5.s2 225.%) a8l5.21ign%5)ed aconc%o ordantlliy >1 times vgn25.52ed co% encroverall aordlignmenantly >t rat1 times e2 all alignment rate5.54% overall alignment rate Processed 30325606 sequences in total Successfully deleted the temporary files zr2096_2_s1_R1_val_1.fq.gz_C_to_T.fastq, zr2096_2_s1_R1_val_1.fq.gz_G_to_A.fastq, zr2096_2_s1_R2_val_2.fq.gz_C_to_T.fastq and zr2096_2_s1_R2_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 30325606 Final Cytosine Methylation Report ================================= Total number of C's analysed: 315022311 Total methylated C's in CpG context: 31591725 Total methylated C's in CHG context: 1577849 Total methylated C's in CHH context: 8697983 Total methylated C's in Unknown context: 538208 Total unmethylated C's in CpG context: 11424690 Total unmethylated C's in CHG context: 70198566 Total unmethylated C's in CHH context: 191531498 Total unmethylated C's in Unknown context: 2352945 C methylated in CpG context: 73.4% C methylated in CHG context: 2.2% C methylated in CHH context: 4.3% C methylated in unknown context (CN or CHN): 18.6% Bismark completed in 0d 4h 23m 11s ==================== Bismark run complete ==================== Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_2_s1_R1_val_1_bismark_bt2_PE_report.html_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_2_s1_R1_val_1_bismark_bt2_PE_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_2_s1_R1_val_1_bismark_bt2_pe.bam_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): /Volumes/Serine/wd/18-04-27/zr2096_3_s1_R1_val_1.fq.gz /Volumes/Serine/wd/18-04-27/zr2096_3_s1_R2_val_2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Current working directory is: /Volumes/Serine/wd/18-05-10 Now reading in and storing sequence information of the genome specified in: /Volumes/Serine/wd/18-03-15/genome/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /Volumes/Serine/wd/18-04-27/zr2096_3_s1_R1_val_1.fq.gz and /Volumes/Serine/wd/18-04-27/zr2096_3_s1_R2_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file zr2096_3_s1_R1_val_1.fq.gz to zr2096_3_s1_R1_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_3_s1_R1_val_1.fq.gz to zr2096_3_s1_R1_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_3_s1_R1_val_1.fq.gz (29548753 sequences in total) Writing a C -> T converted version of the input file zr2096_3_s1_R2_val_2.fq.gz to zr2096_3_s1_R2_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_3_s1_R2_val_2.fq.gz to zr2096_3_s1_R2_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_3_s1_R2_val_2.fq.gz (29548753 sequences in total) Input files are zr2096_3_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_3_s1_R1_val_1.fq.gz_G_to_A.fastq and zr2096_3_s1_R2_val_2.fq.gz_C_to_T.fastq and zr2096_3_s1_R2_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /Volumes/Serine/wd/18-03-15/genome/ with the specified options: -q --score-min L,0,-0.9 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr2096_3_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_3_s1_R2_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.9 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1059:2153_1:N:0:ACAGTG/1 77 * 0 0 * * 0 0 TAATTTAAATAATTTTATATAAATNNNNNNNNNNNNNNNTATTTAAATTAAAAATTTAAATAAATTTTTTTAATTATTTA FFFFFFFFFFFFFFFFFFFFFFFF###############<<>> Writing bisulfite mapping results to zr2096_3_s1_R1_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /Volumes/Serine/wd/18-04-27/zr2096_3_s1_R1_val_1.fq.gz and /Volumes/Serine/wd/18-04-27/zr2096_3_s1_R2_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:2209:16034:32588_1:N:0:ACAGTG NC_007175.2 2 Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far 2295929548725534 reads; 4875897553o4f8 3 threadsr;ee 7s5oa3e:d res ;f tha of the2esdss9e;5 :48e 7: of 25t935 h 4 8e753se(: 1 ( 01020.9500%)480.02095487 75w3er 53%e )p (weair r1(e paire1000edd.;00; o0 of .thf 00these:% %e) sewe) we: re re p2paira1e6i rd03 e21d5; of; of the1450541the1s e:s(e: 721 564 2 69(2.9373.2%1) a 1(162l3igne%0) 7a24ligned .dc co99 n(oc8n73%.18coro)dan rda%ntt) alilagyl 0 tilymn 0ese d icongt imes3c1ned 663 38 con3o (cord10ant.72r%l16) a1yldantlyign0 ed0 0 t conc itme00ord (s1ia0.70 mes%n ) alig nte ly d 314ecxoac n 2c313ordanttll470yy4 (e1 001x80 ti (ac.mtel 64y 1%10 . ) a6 l1%) alitgi4niemedg n ced cononcc ordor83daant1n874l t 4(y16784.3l5% )ye6 1exac 2x a(t1llay6 ign1 cetimd tecl. ony19 c%1 tio)rm de aaln4i7 9g169486 4(tne16.2l172%)y d conalig8 cor>1 dti0anemntd c es(on 16.ly co>1 r3da9t27%.0ntl)7 aimesyl > 1 %it imesgon2 6evd.8 co2e9n%rcoral6.dl al8 2%ao overnigvanlemenrtlalll tal igy nrme>1nt atear at e lignment rate times 27.02% overall alignment rate Processed 29548753 sequences in total Successfully deleted the temporary files zr2096_3_s1_R1_val_1.fq.gz_C_to_T.fastq, zr2096_3_s1_R1_val_1.fq.gz_G_to_A.fastq, zr2096_3_s1_R2_val_2.fq.gz_C_to_T.fastq and zr2096_3_s1_R2_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 29548753 Final Cytosine Methylation Report ================================= Total number of C's analysed: 364333091 Total methylated C's in CpG context: 42231693 Total methylated C's in CHG context: 1748101 Total methylated C's in CHH context: 6570371 Total methylated C's in Unknown context: 473894 Total unmethylated C's in CpG context: 11323986 Total unmethylated C's in CHG context: 81087161 Total unmethylated C's in CHH context: 221371779 Total unmethylated C's in Unknown context: 2480520 C methylated in CpG context: 78.9% C methylated in CHG context: 2.1% C methylated in CHH context: 2.9% C methylated in unknown context (CN or CHN): 16.0% Bismark completed in 0d 4h 29m 43s ==================== Bismark run complete ==================== Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_3_s1_R1_val_1_bismark_bt2_PE_report.html_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_3_s1_R1_val_1_bismark_bt2_PE_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_3_s1_R1_val_1_bismark_bt2_pe.bam_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): /Volumes/Serine/wd/18-04-27/zr2096_4_s1_R1_val_1.fq.gz /Volumes/Serine/wd/18-04-27/zr2096_4_s1_R2_val_2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Current working directory is: /Volumes/Serine/wd/18-05-10 Now reading in and storing sequence information of the genome specified in: /Volumes/Serine/wd/18-03-15/genome/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /Volumes/Serine/wd/18-04-27/zr2096_4_s1_R1_val_1.fq.gz and /Volumes/Serine/wd/18-04-27/zr2096_4_s1_R2_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file zr2096_4_s1_R1_val_1.fq.gz to zr2096_4_s1_R1_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_4_s1_R1_val_1.fq.gz to zr2096_4_s1_R1_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_4_s1_R1_val_1.fq.gz (23970516 sequences in total) Writing a C -> T converted version of the input file zr2096_4_s1_R2_val_2.fq.gz to zr2096_4_s1_R2_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_4_s1_R2_val_2.fq.gz to zr2096_4_s1_R2_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_4_s1_R2_val_2.fq.gz (23970516 sequences in total) Input files are zr2096_4_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_4_s1_R1_val_1.fq.gz_G_to_A.fastq and zr2096_4_s1_R2_val_2.fq.gz_C_to_T.fastq and zr2096_4_s1_R2_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /Volumes/Serine/wd/18-03-15/genome/ with the specified options: -q --score-min L,0,-0.9 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr2096_4_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_4_s1_R2_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.9 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1343:2133_1:N:0:GCCAAT/1 77 * 0 0 * * 0 0 ATAGTGGTTGTTATGGAAATTAGNNNNNNNNNNNNNNNNNNNNNNNNNTGNANTNTTTTTATTAGAATTGTTAAGGTTT FFFFFFFFFFFFFFFFFFFFFFF#########################<<#<#/#<>> Writing bisulfite mapping results to zr2096_4_s1_R1_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /Volumes/Serine/wd/18-04-27/zr2096_4_s1_R1_val_1.fq.gz and /Volumes/Serine/wd/18-04-27/zr2096_4_s1_R2_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:2206:10235:74664_1:N:0:GCCAAT NC_007175.2 17189 Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far 22323939705196707051 reads; of t65 hesereads;1 of6 :thes e:reads; of2 th 32e93se:97051 7 051662 ( (1013900.007%) were pa051ired; of 0.6the0 s(e: 10 %) wer17e 1334000.5 paired(00;% o) w7erf1.4 e thpaires8e:%) al eigned conco d; o173rfd4 a2521t ntly (0 thesi7e:2. 35% ) alim gesned c1 728051382oncor065dantly 0 times78 ( (11.70 71.50% %) aligned ) al i27086gned conc1oco5rdant (l1nc1.ordany3 0 tim0t%lyes ) align e e xac2d79166tl 1 (y1c 1.6on51co%rdant timely ) 4ali exactly 1 time g031 n4 e53d c (oncor16. dant8391l2%)9380y exactly 1 ti a (me16 . ligned 35%) aligc4ned0 406c4oonc8ordantly (>1n16c o.86rdat%nime) astl ilyg28 >1 tn.ed coi5ncom2%re daoventlsry a l>l 1a ligtimes2n7ment ra.6te5 % overa2l 8l .50% ovealignmenrallt rate a lignment rate 23970516 reads; of these: 23970516 (100.00%) were paired; of these: 17339555 (72.34%) aligned concordantly 0 times 2719348 (11.34%) aligned concordantly exactly 1 time 3911613 (16.32%) aligned concordantly >1 times 27.66% overall alignment rate Processed 23970516 sequences in total Successfully deleted the temporary files zr2096_4_s1_R1_val_1.fq.gz_C_to_T.fastq, zr2096_4_s1_R1_val_1.fq.gz_G_to_A.fastq, zr2096_4_s1_R2_val_2.fq.gz_C_to_T.fastq and zr2096_4_s1_R2_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 23970516 Final Cytosine Methylation Report ================================= Total number of C's analysed: 280278413 Total methylated C's in CpG context: 25098800 Total methylated C's in CHG context: 1256491 Total methylated C's in CHH context: 5933670 Total methylated C's in Unknown context: 376207 Total unmethylated C's in CpG context: 11548982 Total unmethylated C's in CHG context: 61411683 Total unmethylated C's in CHH context: 175028787 Total unmethylated C's in Unknown context: 2038992 C methylated in CpG context: 68.5% C methylated in CHG context: 2.0% C methylated in CHH context: 3.3% C methylated in unknown context (CN or CHN): 15.6% Bismark completed in 0d 3h 25m 38s ==================== Bismark run complete ==================== Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_4_s1_R1_val_1_bismark_bt2_PE_report.html_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_4_s1_R1_val_1_bismark_bt2_PE_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_4_s1_R1_val_1_bismark_bt2_pe.bam_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): /Volumes/Serine/wd/18-04-27/zr2096_5_s1_R1_val_1.fq.gz /Volumes/Serine/wd/18-04-27/zr2096_5_s1_R2_val_2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Current working directory is: /Volumes/Serine/wd/18-05-10 Now reading in and storing sequence information of the genome specified in: /Volumes/Serine/wd/18-03-15/genome/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /Volumes/Serine/wd/18-04-27/zr2096_5_s1_R1_val_1.fq.gz and /Volumes/Serine/wd/18-04-27/zr2096_5_s1_R2_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file zr2096_5_s1_R1_val_1.fq.gz to zr2096_5_s1_R1_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_5_s1_R1_val_1.fq.gz to zr2096_5_s1_R1_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_5_s1_R1_val_1.fq.gz (31503281 sequences in total) Writing a C -> T converted version of the input file zr2096_5_s1_R2_val_2.fq.gz to zr2096_5_s1_R2_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_5_s1_R2_val_2.fq.gz to zr2096_5_s1_R2_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_5_s1_R2_val_2.fq.gz (31503281 sequences in total) Input files are zr2096_5_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_5_s1_R1_val_1.fq.gz_G_to_A.fastq and zr2096_5_s1_R2_val_2.fq.gz_C_to_T.fastq and zr2096_5_s1_R2_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /Volumes/Serine/wd/18-03-15/genome/ with the specified options: -q --score-min L,0,-0.9 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr2096_5_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_5_s1_R2_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.9 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1218:2142_1:N:0:CAGATC/1 77 * 0 0 * * 0 0 TTATTTAAATTTTATTATTTATANNNNNNNNNNNNNNNNNNATTNTTTTTATTATATATATAAAATTATTTTAAAATTAT FFFFFFFFFFFFFFFFFFFFFFF##################<<<#<>> Writing bisulfite mapping results to zr2096_5_s1_R1_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /Volumes/Serine/wd/18-04-27/zr2096_5_s1_R1_val_1.fq.gz and /Volumes/Serine/wd/18-04-27/zr2096_5_s1_R2_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:2109:17502:89766_1:N:0:CAGATC NC_007175.2 17173 Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:2116:16897:28912_1:N:0:CAGATC NC_035780.1 1 Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:2311:18572:58643_1:N:0:CAGATC NC_007175.2 17189 Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far 33150321335031503281158218 re1ads;03281 ro feadrres; atds; of these:ofe ads h; of these3 est:he: ese:150 32 3 3150811 (53102030283.108 10(51003281 1 0(.00%%) () we110re pwaeire rep0d;.000 %oa0.) wfirer eed; 0t 0hpae%s) weiredofe;r of th tehs:ee: s e e:p2 3a i7r 995 ed723;8 of 8(172375.5541622 8% (th) easel9:9i4g 75(.6 ne70d 4 .5 c0%%) align2o)3enc4 7d848ao rdacon8ntco lrdlyani(gned 0tly 0 c timeoncots7ird4maens.53 tl % y ) 3 2 03234alig638305 t6nei6mes d( ( 10.10co2.5n27 %% )c a) ali3l3o84r0dantlgy ned6 ig7cnoe0n c tdime(so 10 . r7cdon c33890oa4rdnat84ly %( n1etlx)y e alxaactlyctl 1y0 1 t.iign7 m6e%et i )d a m44ligened 690 6concord c oa nt5 l n4(y 1cordexa45ant55c49.3tl ly (1y 1 e1xactl4ty 1.9 %1i4t) m%al)i aglnigned ceeodinm c coerd aon n t clo y rd4 a6n>465tly >032201 ti1 (514.770me 9s (time261%)s 4.472 aligne%) adlig cnoednc24orda..45 4c0not%nl overa% yoverlallcl al aoi rldantlygi>gnmnme1 netimnt er ta>ts1 e t25 imes. 50% rate2ov5. erall ali47% ognverament lrl ate alignment rate Processed 31503281 sequences in total Successfully deleted the temporary files zr2096_5_s1_R1_val_1.fq.gz_C_to_T.fastq, zr2096_5_s1_R1_val_1.fq.gz_G_to_A.fastq, zr2096_5_s1_R2_val_2.fq.gz_C_to_T.fastq and zr2096_5_s1_R2_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 31503281 Final Cytosine Methylation Report ================================= Total number of C's analysed: 361589489 Total methylated C's in CpG context: 32442365 Total methylated C's in CHG context: 1773523 Total methylated C's in CHH context: 7612648 Total methylated C's in Unknown context: 523192 Total unmethylated C's in CpG context: 13951477 Total unmethylated C's in CHG context: 77101091 Total unmethylated C's in CHH context: 228708385 Total unmethylated C's in Unknown context: 2635231 C methylated in CpG context: 69.9% C methylated in CHG context: 2.2% C methylated in CHH context: 3.2% C methylated in unknown context (CN or CHN): 16.6% Bismark completed in 0d 4h 23m 54s ==================== Bismark run complete ==================== Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_5_s1_R1_val_1_bismark_bt2_PE_report.html_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_5_s1_R1_val_1_bismark_bt2_PE_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_5_s1_R1_val_1_bismark_bt2_pe.bam_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): /Volumes/Serine/wd/18-04-27/zr2096_6_s1_R1_val_1.fq.gz /Volumes/Serine/wd/18-04-27/zr2096_6_s1_R2_val_2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Current working directory is: /Volumes/Serine/wd/18-05-10 Now reading in and storing sequence information of the genome specified in: /Volumes/Serine/wd/18-03-15/genome/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /Volumes/Serine/wd/18-04-27/zr2096_6_s1_R1_val_1.fq.gz and /Volumes/Serine/wd/18-04-27/zr2096_6_s1_R2_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file zr2096_6_s1_R1_val_1.fq.gz to zr2096_6_s1_R1_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_6_s1_R1_val_1.fq.gz to zr2096_6_s1_R1_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_6_s1_R1_val_1.fq.gz (23909493 sequences in total) Writing a C -> T converted version of the input file zr2096_6_s1_R2_val_2.fq.gz to zr2096_6_s1_R2_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_6_s1_R2_val_2.fq.gz to zr2096_6_s1_R2_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_6_s1_R2_val_2.fq.gz (23909493 sequences in total) Input files are zr2096_6_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_6_s1_R1_val_1.fq.gz_G_to_A.fastq and zr2096_6_s1_R2_val_2.fq.gz_C_to_T.fastq and zr2096_6_s1_R2_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /Volumes/Serine/wd/18-03-15/genome/ with the specified options: -q --score-min L,0,-0.9 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr2096_6_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_6_s1_R2_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.9 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1093:2134_1:N:0:CTTGTA/1 77 * 0 0 * * 0 0 TTAATTTTATTATTAAATAAAAANNNNNNNNNNNNNNNNNNNNNNANNTANANAAATATTAATTAAATATTTTTAAAATA FFFFFFFFFFFFFFFFFFFFFFF######################<##<<#<#<>> Writing bisulfite mapping results to zr2096_6_s1_R1_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /Volumes/Serine/wd/18-04-27/zr2096_6_s1_R1_val_1.fq.gz and /Volumes/Serine/wd/18-04-27/zr2096_6_s1_R2_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1201:7258:96604_1:N:0:CTTGTA NC_035780.1 1 Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far 23909493239 re20a9394932d30 9sr90e;94 a94o3d 9fs;3 t rh oerefeas taeds;d: of thsh ; oee fss e:239 th0e e9:se: 4 9323 (909491 320 23(0.09310900090%9) w4.934 93 0ere p0(%) air(ewed; of tre100. h10eps00.00%)ai0re ew:de%) we; ofre paitrhes e174e:13rde 592; p(oaire7 f1d2.74105;818 (of3% 7) alith 2tehg.n82%) aleeisesdge:: con co ned cornd1697ca0 nord9tly 80 4 (tim70.ea9sn t8l %16)y96 a4337 l ( ign 7 0e d0263470 .c1onc toirdan95%mest)l (y1 a 0 1 .ti0lig2m%es)2 6 46 an3 7el0d co2inc 8(111g.07n8%e6)97 o ardli(gnead cdn o1n1.tccly 07oo9% r)d tncoraadantlnitlyl miexagycnete lsy d co ne1 t ci 2ordantlyx eamxacctly833094te l 1 t y( im13e1.8 86121 5 0%ti3me8 5) 2 504 2 41a(1198(6112.15 %6(.1) alli1%gined concg) ordanligned ant1con7c.23leo%dry >d 1a) alconntly >1 ttimciegnesi m27eosdr .17 cdao2nncord7.ant1t%l8y oly v>%eral 1 ol ali evegrall alinxmenactgntlmt rimeatsye e29 1 tinmet r . ate 02% over al4112062 (l alignment rate 17.20%) aligned concordantly >1 times 29.05% overall alignment rate Processed 23909493 sequences in total Successfully deleted the temporary files zr2096_6_s1_R1_val_1.fq.gz_C_to_T.fastq, zr2096_6_s1_R1_val_1.fq.gz_G_to_A.fastq, zr2096_6_s1_R2_val_2.fq.gz_C_to_T.fastq and zr2096_6_s1_R2_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 23909493 Final Cytosine Methylation Report ================================= Total number of C's analysed: 282996812 Total methylated C's in CpG context: 28611304 Total methylated C's in CHG context: 1285013 Total methylated C's in CHH context: 5824036 Total methylated C's in Unknown context: 405402 Total unmethylated C's in CpG context: 9216526 Total unmethylated C's in CHG context: 61793875 Total unmethylated C's in CHH context: 176266058 Total unmethylated C's in Unknown context: 2109962 C methylated in CpG context: 75.6% C methylated in CHG context: 2.0% C methylated in CHH context: 3.2% C methylated in unknown context (CN or CHN): 16.1% Bismark completed in 0d 3h 28m 27s ==================== Bismark run complete ==================== Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_6_s1_R1_val_1_bismark_bt2_PE_report.html_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_6_s1_R1_val_1_bismark_bt2_PE_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_6_s1_R1_val_1_bismark_bt2_pe.bam_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): /Volumes/Serine/wd/18-04-27/zr2096_7_s1_R1_val_1.fq.gz /Volumes/Serine/wd/18-04-27/zr2096_7_s1_R2_val_2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Current working directory is: /Volumes/Serine/wd/18-05-10 Now reading in and storing sequence information of the genome specified in: /Volumes/Serine/wd/18-03-15/genome/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /Volumes/Serine/wd/18-04-27/zr2096_7_s1_R1_val_1.fq.gz and /Volumes/Serine/wd/18-04-27/zr2096_7_s1_R2_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file zr2096_7_s1_R1_val_1.fq.gz to zr2096_7_s1_R1_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_7_s1_R1_val_1.fq.gz to zr2096_7_s1_R1_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_7_s1_R1_val_1.fq.gz (29273635 sequences in total) Writing a C -> T converted version of the input file zr2096_7_s1_R2_val_2.fq.gz to zr2096_7_s1_R2_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_7_s1_R2_val_2.fq.gz to zr2096_7_s1_R2_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_7_s1_R2_val_2.fq.gz (29273635 sequences in total) Input files are zr2096_7_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_7_s1_R1_val_1.fq.gz_G_to_A.fastq and zr2096_7_s1_R2_val_2.fq.gz_C_to_T.fastq and zr2096_7_s1_R2_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /Volumes/Serine/wd/18-03-15/genome/ with the specified options: -q --score-min L,0,-0.9 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr2096_7_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_7_s1_R2_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.9 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1132:2189_1:N:0:ATCACG/1 77 * 0 0 * * 0 0 TTATTATGATGAATTTAAATATTAATAATAAAATTTAAAAAAAATATAAATGTTAAATATTAAATTTTTTAAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP HWI-C00124:321:CC781ANXX:1:1101:1132:2189_2:N:0:ATCACG/2 141 * 0 0 * * 0 0 TTTTTAAAAAATTTAATATTTAACATTTATATTTTTTTTAAATTTTATTATTAATATTTAAATTCATCATAATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF/FFBBFFFFFFBBFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr2096_7_s1_R1_val_1.fq.gz_G_to_A.fastq and zr2096_7_s1_R2_val_2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.9 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1132:2189_1:N:0:ATCACG/1 99 NC_035781.1_GA_converted 24539756 6 75M = 24539756 -75 CTACTACAACAAATTCAAATATTAATAACAAAATTTAAAAAAAACATAAACATTAAATATCAAATTCTTCAAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:75 YS:i:0 YT:Z:CP HWI-C00124:321:CC781ANXX:1:1101:1132:2189_2:N:0:ATCACG/2 147 NC_035781.1_GA_converted 24539756 6 75M = 24539756 -75 CTACTACAACAAATTCAAATATTAATAACAAAATTTAAAAAAAACATAAACATTAAATATCAAATTCTTCAAAAA FFFFFFFFFFFFFBBFFFFFFBBFF/FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:75 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr2096_7_s1_R1_val_1.fq.gz_G_to_A.fastq and zr2096_7_s1_R2_val_2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.9 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1132:2189_1:N:0:ATCACG/1 83 NC_035780.1_CT_converted 42548691 6 75M = 42548691 -75 TTTTTGAAGAATTTGATATTTAATGTTTATGTTTTTTTTAAATTTTGTTATTAATATTTGAATTTGTTGTAGTAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:75 YS:i:0 YT:Z:CP HWI-C00124:321:CC781ANXX:1:1101:1132:2189_2:N:0:ATCACG/2 163 NC_035780.1_CT_converted 42548691 6 75M = 42548691 -75 TTTTTGAAGAATTTGATATTTAATGTTTATGTTTTTTTTAAATTTTGTTATTAATATTTGAATTTGTTGTAGTAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF/FFBBFFFFFFBBFFFFFFFFFFFFF AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:75 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr2096_7_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_7_s1_R2_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.9 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1132:2189_1:N:0:ATCACG/1 77 * 0 0 * * 0 0 TTATTATGATGAATTTAAATATTAATAATAAAATTTAAAAAAAATATAAATGTTAAATATTAAATTTTTTAAAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP HWI-C00124:321:CC781ANXX:1:1101:1132:2189_2:N:0:ATCACG/2 141 * 0 0 * * 0 0 TTTTTAAAAAATTTAATATTTAACATTTATATTTTTTTTAAATTTTATTATTAATATTTAAATTCATCATAATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF/FFBBFFFFFFBBFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to zr2096_7_s1_R1_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /Volumes/Serine/wd/18-04-27/zr2096_7_s1_R1_val_1.fq.gz and /Volumes/Serine/wd/18-04-27/zr2096_7_s1_R2_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:2209:9828:53780_1:N:0:ATCACG NC_007175.2 17175 Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:2211:12726:18562_1:N:0:ATCACG NC_007175.2 17178 Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:2309:5099:43290_1:N:0:ATCACG NC_035788.1 1 Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far 2292729363592 r2736e73ads363;55 r readse; ofaod thesse:; o ff t2 heth9se27se:e3635 (:10 0. 200%92 ) we73623r952736e ( 315 (p1000a.00ired; %of)0.0 we thre0e%s pae:i red;) we r oe pai2rf these22e:59857d; of these: ( 76. 0 22 420922089528%7) a8597li97 g n((e773d6 355.con5 4.9rc4o%6eads)%r) aldai;anglined g ctnoneocord cdaoncfly ordantn ttlhey s0 e0:ly 0 t imes ti mes t3 im209360270es6 23362953 (635(110 .(470.%)1 260%0.03) 007ali%ag9l) wned63i 5e gconcrn(e 1peaord0d.ai52 contlr%y) e xaalcend;ti lcoof thgned cyredos 1 eatncntlimy exaec: toly 1 4rd01t i1am 322e2n68t4ly 2 ex 33 (a c213.tl7401%0869 y 1 ti)6m e((al14ign. 76.04e 06d%% c) alignonc e)d alcorda4o1n0nciotgly 54rd01a >ne(1d1 concntlt4imy >.10 tio2rdaesm% ) alies2ngn3 .29e4d.t c6ly 0 tim5e1s%% ooncordan tv elo r yal vel r al>a1 iltilmes agnl2mi9gent rat9e5 n228men9 4t( rate1 0.23%) al.54% overall alignment rate igned concordantly exactly 1 time 4014114 (13.71%) aligned concordantly >1 times 23.94% overall alignment rate Processed 29273635 sequences in total Successfully deleted the temporary files zr2096_7_s1_R1_val_1.fq.gz_C_to_T.fastq, zr2096_7_s1_R1_val_1.fq.gz_G_to_A.fastq, zr2096_7_s1_R2_val_2.fq.gz_C_to_T.fastq and zr2096_7_s1_R2_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 29273635 Final Cytosine Methylation Report ================================= Total number of C's analysed: 341004922 Total methylated C's in CpG context: 32577834 Total methylated C's in CHG context: 1766331 Total methylated C's in CHH context: 6993913 Total methylated C's in Unknown context: 458498 Total unmethylated C's in CpG context: 11423070 Total unmethylated C's in CHG context: 73901290 Total unmethylated C's in CHH context: 214342484 Total unmethylated C's in Unknown context: 2434460 C methylated in CpG context: 74.0% C methylated in CHG context: 2.3% C methylated in CHH context: 3.2% C methylated in unknown context (CN or CHN): 15.8% Bismark completed in 0d 4h 9m 52s ==================== Bismark run complete ==================== Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_7_s1_R1_val_1_bismark_bt2_PE_report.html_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_7_s1_R1_val_1_bismark_bt2_PE_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_7_s1_R1_val_1_bismark_bt2_pe.bam_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): /Volumes/Serine/wd/18-04-27/zr2096_8_s1_R1_val_1.fq.gz /Volumes/Serine/wd/18-04-27/zr2096_8_s1_R2_val_2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Current working directory is: /Volumes/Serine/wd/18-05-10 Now reading in and storing sequence information of the genome specified in: /Volumes/Serine/wd/18-03-15/genome/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /Volumes/Serine/wd/18-04-27/zr2096_8_s1_R1_val_1.fq.gz and /Volumes/Serine/wd/18-04-27/zr2096_8_s1_R2_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file zr2096_8_s1_R1_val_1.fq.gz to zr2096_8_s1_R1_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_8_s1_R1_val_1.fq.gz to zr2096_8_s1_R1_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_8_s1_R1_val_1.fq.gz (29483218 sequences in total) Writing a C -> T converted version of the input file zr2096_8_s1_R2_val_2.fq.gz to zr2096_8_s1_R2_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_8_s1_R2_val_2.fq.gz to zr2096_8_s1_R2_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_8_s1_R2_val_2.fq.gz (29483218 sequences in total) Input files are zr2096_8_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_8_s1_R1_val_1.fq.gz_G_to_A.fastq and zr2096_8_s1_R2_val_2.fq.gz_C_to_T.fastq and zr2096_8_s1_R2_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /Volumes/Serine/wd/18-03-15/genome/ with the specified options: -q --score-min L,0,-0.9 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr2096_8_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_8_s1_R2_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.9 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:1:1101:1281:2170_1:N:0:TTAGGC/1 77 * 0 0 * * 0 0 TTAAAAAATTTATTAAATTTATTATTATTTNTTATTTTTTATAAAAGAAAATAGAGAGAGAGAGAGAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#<>> Writing bisulfite mapping results to zr2096_8_s1_R1_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /Volumes/Serine/wd/18-04-27/zr2096_8_s1_R1_val_1.fq.gz and /Volumes/Serine/wd/18-04-27/zr2096_8_s1_R2_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1112:2054:25809_1:Y:0:TTAGGC NC_007175.2 17197 Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1208:16282:90212_1:N:0:TTAGGC NC_007175.2 1 Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1301:18980:18166_1:Y:0:TTAGGC NC_007175.2 17175 Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1304:9180:4925_1:N:0:TTAGGC NC_007175.2 17172 Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:1311:7196:8646_1:N:0:TTAGGC NC_007175.2 1 Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:2112:7223:18290_1:N:0:TTAGGC NC_007175.2 17197 Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:1:2303:6577:56043_1:N:0:TTAGGC NC_007175.2 17170 Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far 2948321822949482 389234r21e818321 r88 reaead dsad; rss;eo a; dsfo;o ff otttf hhteheseeh:se: 29se e4s: e :2948 832 122832941883 ((10100.020.19000%84)%8 (wer10e)0 3 wp.ea02re0i 1%pr8)ea d;wi e(red10; orof0e f t phtaeh.iresesede:; :o f0 t 0 %22h )2299e38se14:53 7 ( 2277773732.7 w8520( (77.8777%e%.) 24al%r)ig anelid gncoednc corond)ca oentra plildgay na0eni ttdil mycreso 0 t ni c27or9md4ea8se0 d0 n ; (t9.ly4 28 of0% 8 t06i)2tme2 sha el s6i g e(n9.ed5 22c:886o%4n )c2 ora1d la(i9.gn79en %d ) ctaol liyn g22ne coed xacocrdtlanync 1or tdaimntetl7 ly y 5 e x3exa74730686acctly (2511t (ly 77.12. 619t%5imet%) ima l)e i 337388gned conc23048549 ali(ordag (112ntly 0ned2. . co9t6i7mes8%% )n) align 2ecaod conc89rlign5e3od1rda0n (t dly >9a.82c1n% tonc)lto irdamaneyst >lligney1 > d12 t2im.7ti6e%mescs o2n222.2. 1c3o%0 voe%o overall avrall laieralllrig gnmandlmeient gnrantnalmtet e ry exactly nta1 ttei rmea t383e 0483 (12.99%) aligned concordantly >1 times 22.81% overall alignment rate Processed 29483218 sequences in total Successfully deleted the temporary files zr2096_8_s1_R1_val_1.fq.gz_C_to_T.fastq, zr2096_8_s1_R1_val_1.fq.gz_G_to_A.fastq, zr2096_8_s1_R2_val_2.fq.gz_C_to_T.fastq and zr2096_8_s1_R2_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 29483218 Final Cytosine Methylation Report ================================= Total number of C's analysed: 304758678 Total methylated C's in CpG context: 25826175 Total methylated C's in CHG context: 1569936 Total methylated C's in CHH context: 7289421 Total methylated C's in Unknown context: 452413 Total unmethylated C's in CpG context: 11727668 Total unmethylated C's in CHG context: 65976027 Total unmethylated C's in CHH context: 192369451 Total unmethylated C's in Unknown context: 2222749 C methylated in CpG context: 68.8% C methylated in CHG context: 2.3% C methylated in CHH context: 3.7% C methylated in unknown context (CN or CHN): 16.9% Bismark completed in 0d 3h 52m 32s ==================== Bismark run complete ==================== Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_8_s1_R1_val_1_bismark_bt2_PE_report.html_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_8_s1_R1_val_1_bismark_bt2_PE_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_8_s1_R1_val_1_bismark_bt2_pe.bam_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): /Volumes/Serine/wd/18-04-27/zr2096_9_s1_R1_val_1.fq.gz /Volumes/Serine/wd/18-04-27/zr2096_9_s1_R2_val_2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Current working directory is: /Volumes/Serine/wd/18-05-10 Now reading in and storing sequence information of the genome specified in: /Volumes/Serine/wd/18-03-15/genome/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /Volumes/Serine/wd/18-04-27/zr2096_9_s1_R1_val_1.fq.gz and /Volumes/Serine/wd/18-04-27/zr2096_9_s1_R2_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file zr2096_9_s1_R1_val_1.fq.gz to zr2096_9_s1_R1_val_1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_9_s1_R1_val_1.fq.gz to zr2096_9_s1_R1_val_1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_9_s1_R1_val_1.fq.gz (31847541 sequences in total) Writing a C -> T converted version of the input file zr2096_9_s1_R2_val_2.fq.gz to zr2096_9_s1_R2_val_2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr2096_9_s1_R2_val_2.fq.gz to zr2096_9_s1_R2_val_2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr2096_9_s1_R2_val_2.fq.gz (31847541 sequences in total) Input files are zr2096_9_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_9_s1_R1_val_1.fq.gz_G_to_A.fastq and zr2096_9_s1_R2_val_2.fq.gz_C_to_T.fastq and zr2096_9_s1_R2_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /Volumes/Serine/wd/18-03-15/genome/ with the specified options: -q --score-min L,0,-0.9 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr2096_9_s1_R1_val_1.fq.gz_C_to_T.fastq and zr2096_9_s1_R2_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.9 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-C00124:321:CC781ANXX:2:1101:1135:2128_1:N:0:ACTTGA/1 77 * 0 0 * * 0 0 AAAATAATAAATAATAAATTANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN >> Writing bisulfite mapping results to zr2096_9_s1_R1_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /Volumes/Serine/wd/18-04-27/zr2096_9_s1_R1_val_1.fq.gz and /Volumes/Serine/wd/18-04-27/zr2096_9_s1_R2_val_2.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:2:2207:4799:56169_1:N:0:ACTTGA NC_007175.2 17167 Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-C00124:321:CC781ANXX:2:2213:18183:81000_1:N:0:ACTTGA NC_007175.2 17188 Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far 318475413331847 5r4111ead 8rea8447d75415s 41 reads;; rose aof tdfs; o thhfeese:; ste 318of:4h 7541e se:(t 1h3 e se:311 88470047.05 0541% ()1041 30 1w(ere84 71.00005%.paired; 00)41%of these wer ()1: 0 we e0 rpaie.r e2pd0;a0%) were paired; o44i of37478 (rf76ed; .t7 3%) ohf talitghenessed coeenh: c: o rd aen st e:24l 2y 4 03 32535t3457i245me0 (s7647056 ( 37 .72( 7% )3330835.97.9 %4a%) 5)5 align (ed9 colnigned.6a8li %)ccordant goly neda 0 tligncieomdnn cecoscon r d3ca4oontl8y 0r35 d0rdanttialy exa4 n(cmettly1 s 10 ti.lmey 0 9344%t)5844 i0a mes (431 206508. 86 %() a1ll3.ii5g39gnned c0ed% ) aliogneconcon6c48d coorndc8arodanr8tldyann ttexly >1 tilmesayctly e1 23.2x(a cttimle 9 . 624837209%y % 1o8 tver (iall me15 a) lali.ig n1 7g %ednm) c481e ntal 6oirncgateo3rd92 (n15.ae1nd 2 contly%cordan)tly a exl>actly 1 1itimeg n te d c iomes n2436.03%c49 over2aorlld aa28lignm (ent nt13.ly >1 t66%) alraigned ctioncomees rdantly >1 tim26.es06 % overall alignment rate 23.28% overall alignment rate Processed 31847541 sequences in total Successfully deleted the temporary files zr2096_9_s1_R1_val_1.fq.gz_C_to_T.fastq, zr2096_9_s1_R1_val_1.fq.gz_G_to_A.fastq, zr2096_9_s1_R2_val_2.fq.gz_C_to_T.fastq and zr2096_9_s1_R2_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 31847541 Final Cytosine Methylation Report ================================= Total number of C's analysed: 375598399 Total methylated C's in CpG context: 42083769 Total methylated C's in CHG context: 2085711 Total methylated C's in CHH context: 7546129 Total methylated C's in Unknown context: 534690 Total unmethylated C's in CpG context: 11443603 Total unmethylated C's in CHG context: 82564185 Total unmethylated C's in CHH context: 229875002 Total unmethylated C's in Unknown context: 2658200 C methylated in CpG context: 78.6% C methylated in CHG context: 2.5% C methylated in CHH context: 3.2% C methylated in unknown context (CN or CHN): 16.7% Bismark completed in 0d 4h 30m 59s ==================== Bismark run complete ==================== Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_9_s1_R1_val_1_bismark_bt2_PE_report.html_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_9_s1_R1_val_1_bismark_bt2_PE_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_9_s1_R1_val_1_bismark_bt2_pe.bam_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify! Bowtie seems to be working fine (tested command '/Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/Applications/bioinfo/samtools-1.3.1/samtools' Reference genome folder provided is /Volumes/Serine/wd/18-03-15/genome/ (absolute path is '/Volumes/Serine/wd/18-03-15/genome/)' Input files to be analysed (in current folder '/Volumes/Serine/wd/18-05-10'): Supplied filename '/Volumes/Serine/wd/18-04-27/zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplication_report.txt_s1_R1_val_1.fq.gz' does not exist, please respecify!