Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.5.2]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/modules/uri_apps/software/SAMtools/1.14-GCC-11.2.0/bin/samtools' Reference genome folder provided is ../data/ (absolute path is '/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/data/)' FastQ format assumed (by default) Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Each Bowtie 2 instance is going to be run with 48 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/code'): ../output/01.00-D-Apul-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_ACR-173-TP2_S4_R1_001.fastq.gz ../output/01.00-D-Apul-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_ACR-173-TP2_S4_R2_001.fastq.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 Output will be written into the directory: /scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/ Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-1.0 -p 48 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/code Now reading in and storing sequence information of the genome specified in: /scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/data/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are ../output/01.00-D-Apul-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_ACR-173-TP2_S4_R1_001.fastq.gz and ../output/01.00-D-Apul-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_ACR-173-TP2_S4_R2_001.fastq.gz Input files are in FastQ format Writing a C -> T converted version of the input file trimmed_ACR-173-TP2_S4_R1_001.fastq.gz to trimmed_ACR-173-TP2_S4_R1_001.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file trimmed_ACR-173-TP2_S4_R1_001.fastq.gz to trimmed_ACR-173-TP2_S4_R1_001.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file trimmed_ACR-173-TP2_S4_R1_001.fastq.gz (213856184 sequences in total) Writing a C -> T converted version of the input file trimmed_ACR-173-TP2_S4_R2_001.fastq.gz to trimmed_ACR-173-TP2_S4_R2_001.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file trimmed_ACR-173-TP2_S4_R2_001.fastq.gz to trimmed_ACR-173-TP2_S4_R2_001.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file trimmed_ACR-173-TP2_S4_R2_001.fastq.gz (213856184 sequences in total) Input files are trimmed_ACR-173-TP2_S4_R1_001.fastq.gz_C_to_T.fastq and trimmed_ACR-173-TP2_S4_R1_001.fastq.gz_G_to_A.fastq and trimmed_ACR-173-TP2_S4_R2_001.fastq.gz_C_to_T.fastq and trimmed_ACR-173-TP2_S4_R2_001.fastq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/data/ with the specified options: -q --score-min L,0,-1.0 -p 48 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from trimmed_ACR-173-TP2_S4_R1_001.fastq.gz_C_to_T.fastq and trimmed_ACR-173-TP2_S4_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.0 -p 48 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00260:131:22L7V3LT4:3:1101:4698:1014_1:N:0:TGCATTCT+CNAGCTAG/1 77 * 0 0 * * 0 0 TNATATTAAAAATAATTATTAAATATTTAAATAAATAATTTTATAAATATAAAATATTTTATATTTTAT I#II9IIIIIIIII9III9IIIII-I9IIIIIIIIIIIIIIIII9IIIIII9IIIII9I9IIIII-III YT:Z:UP LH00260:131:22L7V3LT4:3:1101:4698:1014_2:N:0:TGCATTCT+CNAGCTAG/2 141 * 0 0 * * 0 0 ANAAAATATAAAATATTTTATATTTATAAAATTATTTATTTAAATATTTAATAATTATTTTTAATATAA I#IIIII9-IIIIIII9IIIIIIIIIII-II-99IIII9IIIIII9-III-9IIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from trimmed_ACR-173-TP2_S4_R1_001.fastq.gz_G_to_A.fastq and trimmed_ACR-173-TP2_S4_R2_001.fastq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-1.0 -p 48 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00260:131:22L7V3LT4:3:1101:4698:1014_1:N:0:TGCATTCT+CNAGCTAG/1 99 ptg000021l_GA_converted 19292318 42 69M = 19292318 69 CNACATCAAAAATAATCATTAAATACTTAAACAAACAATTTCACAAATATAAAATATCCCATACTCTAC I#II9IIIIIIIII9III9IIIII-I9IIIIIIIIIIIIIIIII9IIIIII9IIIII9I9IIIII-III AS:i:-7 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:1T39T27 YS:i:-7 YT:Z:CP LH00260:131:22L7V3LT4:3:1101:4698:1014_2:N:0:TGCATTCT+CNAGCTAG/2 147 ptg000021l_GA_converted 19292318 42 69M = 19292318 -69 CTACATCAAAAATAATCATTAAATACTTAAACAAACAATTTCACAAATATAAAATATCCCATACTCTNC IIIIIIIIIIIIIIIII9-III-9IIIIII9IIII99-II-IIIIIIIIIII9IIIIIII-9IIIII#I AS:i:-7 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:41T25A1 YS:i:-7 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from trimmed_ACR-173-TP2_S4_R1_001.fastq.gz_G_to_A.fastq and trimmed_ACR-173-TP2_S4_R2_001.fastq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-1.0 -p 48 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00260:131:22L7V3LT4:3:1101:4698:1014_1:N:0:TGCATTCT+CNAGCTAG/1 77 * 0 0 * * 0 0 CNACATCAAAAATAATCATTAAATACTTAAACAAACAATTTCACAAATATAAAATATCCCATACTCTAC I#II9IIIIIIIII9III9IIIII-I9IIIIIIIIIIIIIIIII9IIIIII9IIIII9I9IIIII-III YT:Z:UP LH00260:131:22L7V3LT4:3:1101:4698:1014_2:N:0:TGCATTCT+CNAGCTAG/2 141 * 0 0 * * 0 0 GNAGAGTATGGGATATTTTATATTTGTGAAATTGTTTGTTTAAGTATTTAATGATTATTTTTGATGTAG I#IIIII9-IIIIIII9IIIIIIIIIII-II-99IIII9IIIIII9-III-9IIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from trimmed_ACR-173-TP2_S4_R1_001.fastq.gz_C_to_T.fastq and trimmed_ACR-173-TP2_S4_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.0 -p 48 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00260:131:22L7V3LT4:3:1101:4698:1014_1:N:0:TGCATTCT+CNAGCTAG/1 77 * 0 0 * * 0 0 TNATATTAAAAATAATTATTAAATATTTAAATAAATAATTTTATAAATATAAAATATTTTATATTTTAT I#II9IIIIIIIII9III9IIIII-I9IIIIIIIIIIIIIIIII9IIIIII9IIIII9I9IIIII-III YT:Z:UP LH00260:131:22L7V3LT4:3:1101:4698:1014_2:N:0:TGCATTCT+CNAGCTAG/2 141 * 0 0 * * 0 0 ANAAAATATAAAATATTTTATATTTATAAAATTATTTATTTAAATATTTAATAATTATTTTTAATATAA I#IIIII9-IIIIIII9IIIIIIIIIII-II-99IIII9IIIIII9-III-9IIIIIIIIIIIIIIIII YT:Z:UP >>> Writing bisulfite mapping results to trimmed_ACR-173-TP2_S4_pe.bam <<< Reading in the sequence files ../output/01.00-D-Apul-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_ACR-173-TP2_S4_R1_001.fastq.gz and ../output/01.00-D-Apul-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_ACR-173-TP2_S4_R2_001.fastq.gz Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1103:19766:3956_1:N:0:GGCATTCT+CAAGCTAG ntLink_7 2 Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1110:10816:23286_1:N:0:GGCATTCT+CAAGCTAG ptg000033l 2625659 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1110:10808:23300_1:N:0:GGCATTCT+CAAGCTAG ptg000033l 2625659 Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1111:48493:23959_1:N:0:GGCATTCT+CAAGCTAG ptg000130l 1 Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1123:31492:21675_1:N:0:GGCATTCT+CAAGCTAG ptg000093l 1 Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1127:45863:12879_1:N:0:GGCATTCT+CAAGCTAG ptg000033l 2625624 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1128:3395:20807_1:N:0:GGCATTCT+CAAGCTAG ptg000033l 2625658 Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1133:25123:1798_1:N:0:GGCATTCT+CAAGCTAG ptg000033l 2625630 Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1146:33879:23651_1:N:0:GGCATTCT+CAAGCTAG ptg000174l 27198 Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1149:51811:13257_1:N:0:GGCATTCT+CAAGCTAG ptg000025l 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1151:29897:26368_1:N:0:GGCATTCT+CAAGCTAG ptg000033l 2625577 Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1162:20834:12753_1:N:0:GGCATTCT+CAAGCTAG ptg000008l 38432908 Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1165:4180:17067_1:N:0:GGCATTCT+TAAGCTAG ptg000127l 27792 Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1177:11164:12991_1:N:0:GGCATTCT+CAAGCTAG ptg000033l 2625606 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1178:33523:27068_1:N:0:GGCATTCT+CAAGCTAG ptg000093l 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1178:33531:27082_1:N:0:GGCATTCT+CAAGCTAG ptg000093l 1 Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1186:5168:18216_1:N:0:GGCATTCT+CAAGCTAG ptg000082l 1 Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1190:41332:5595_1:N:0:GGCATTCT+CAAGCTAG ptg000093l 1 Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1196:22817:1644_1:N:0:GGCATTCT+CAAGCTAG ptg000033l 2625606 Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1205:32430:12178_1:N:0:GGCATTCT+CAAGCTAG ptg000109l 39590 Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1210:22307:9026_1:N:0:GGCATTCT+CAAGCTAG ptg000095l 40198 Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1213:29614:5651_1:N:0:GGCATTCT+CAAGCTAG ptg000033l 2625613 Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1216:40353:17683_1:N:0:GGCATTCT+CAAGCTAG ptg000092l 29039 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1217:49359:13719_1:N:0:GGCATTCT+CAAGCTAG ptg000033l 2625580 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1217:49351:13733_1:N:0:GGCATTCT+CAAGCTAG ptg000033l 2625580 Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1223:12038:15316_1:N:0:GGCATTCT+CAAGCTAG ptg000137l 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1224:21206:5805_1:N:0:GGCATTCT+CAAGCTAG ptg000093l 1 Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1227:7004:27531_1:N:0:GGCATTCT+CAAGCTAG ptg000109l 39607 Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1231:32236:3970_1:N:0:GGCATTCT+CAAGCTAG ptg000146l 1 Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1243:15169:15946_1:N:0:GGCATTCT+CAAGCTAG ptg000008l 38432913 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1246:45386:18075_1:N:0:GGCATTCT+CAAGCTAG ptg000063l 30336 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1246:45386:18104_1:N:0:GGCATTCT+CAAGCTAG ptg000063l 30336 Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1247:44528:19868_1:N:0:GGCATTCT+CAAGCTAG ptg000033l 2625606 Processed 41000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1253:1979:18776_1:N:0:GGCATTCT+CAAGCTAG ptg000113l 2 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1253:1971:18790_1:N:0:GGCATTCT+CAAGCTAG ptg000113l 1 Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1257:23076:15792_1:N:0:GGCATTAT+CAAGCTAG ptg000033l 2625576 Processed 43000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1258:7450:19812_1:N:0:GGCATTCT+CAAGCTAG ptg000093l 1 Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1266:28530:27335_1:N:0:GGCATTCT+CAAGCTAG ptg000033l 2625621 Processed 46000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1269:49367:28497_1:N:0:GGCATTCT+CAAGCTAG ptg000125l 18922 Processed 47000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1274:44997:17907_1:N:0:GGCATTCT+CAAGCTAG ptg000106l 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1275:35481:2387_1:N:0:GGCATTCT+CAAGCTAG ptg000146l 1 Processed 48000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1276:6130:10273_1:N:0:GGCATTAT+CAAGCTAG ptg000095l 40194 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1276:6139:10287_1:N:0:GGCATTCT+CAAGCTAG ptg000095l 40194 Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1288:11609:10287_1:N:0:GGCATTCT+CAAGCTAG ptg000109l 39607 Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1298:10427:10932_1:N:0:GGCATTCT+CAAGCTAG ptg000109l 39608 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1301:24783:8354_1:N:0:GGCATTCT+CAAGCTAG ptg000033l 2625617 Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1305:19863:27629_1:N:0:GGCATTCT+CAAGCTAG ptg000033l 2625649 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1306:6446:6505_1:N:0:GGCATTCT+CAAGCTAG ptg000122l 1 Processed 57000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1311:33361:22726_1:N:0:GGCATTCT+CAAGCTAG ptg000033l 2625650 Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1324:48048:1981_1:N:0:GGCATTCT+CAAGCTAG ptg000033l 2625572 Processed 62000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1328:5192:3213_1:N:0:AGCATTCT+CAAGCTAG ntLink_4 1 Processed 63000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1330:8550:28329_1:N:0:GGCATTCT+CAAGCTAG ptg000033l 2625657 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1332:3468:9587_1:N:0:GGCATTCT+CAAGCTAG ptg000093l 1 Processed 64000000 sequence pairs so far Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 67000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1346:22695:5020_1:N:0:GGCATTCT+CAAGCTAG ptg000027l 2 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1349:29088:15666_1:N:0:GGCATTCT+CAAGCTAG ptg000109l 39606 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1349:29104:15666_1:N:0:GGCATTCT+CAAGCTAG ptg000109l 39606 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1349:29096:15680_1:N:0:GGCATTCT+CAAGCTAG ptg000109l 39606 Processed 68000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1350:22614:17039_1:N:0:GGCATTCT+CAAGCTAG ptg000123l 44459 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1352:26013:23342_1:N:0:GGCATTCT+CAAGCTAG ptg000006l 1 Processed 69000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1353:39802:23763_1:N:0:GGCATTCT+CAAGCTAG ptg000082l 1 Processed 70000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1359:19232:21746_1:N:0:GGCATTCT+CAAGCTAG ptg000069l 259768 Processed 71000000 sequence pairs so far Processed 72000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1364:13244:13705_1:N:0:GGCATTCT+CAAGCTAG ptg000109l 39611 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1364:13235:13719_1:N:0:GGCATTCT+CAAGCTAG ptg000109l 39611 Processed 73000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1368:30221:12977_1:N:0:GGCATTAT+CAAGCTAG ptg000069l 259767 Processed 74000000 sequence pairs so far Processed 75000000 sequence pairs so far Processed 76000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1379:37091:4334_1:N:0:GGCATTCT+CAAGCTAG ptg000006l 3 Processed 77000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1384:13980:18118_1:N:0:AGCATTCT+CAAGCTAG ptg000093l 1 Processed 78000000 sequence pairs so far Processed 79000000 sequence pairs so far Processed 80000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1394:40207:9783_1:N:0:GGCATTCT+CAAGCTAG ptg000033l 2625572 Processed 81000000 sequence pairs so far Processed 82000000 sequence pairs so far Processed 83000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1407:42602:14237_1:N:0:GGCATTCT+CAAGCTAG ptg000123l 44445 Processed 84000000 sequence pairs so far Processed 85000000 sequence pairs so far Processed 86000000 sequence pairs so far Processed 87000000 sequence pairs so far Processed 88000000 sequence pairs so far Processed 89000000 sequence pairs so far Processed 90000000 sequence pairs so far Processed 91000000 sequence pairs so far Processed 92000000 sequence pairs so far Processed 93000000 sequence pairs so far Processed 94000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1445:4407:3115_1:N:0:GGCATTCT+CAAGCTAG ptg000130l 1 Processed 95000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1447:43695:13579_1:N:0:GGCATTCT+CAAGCTAG ptg000033l 2625636 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1448:4205:2849_1:N:0:GGCATTCT+CAAGCTAG ptg000033l 2625572 Processed 96000000 sequence pairs so far Processed 97000000 sequence pairs so far Processed 98000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1460:21036:6827_1:N:0:GGCATTCT+CAAGCTAG ptg000033l 2625606 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1461:38378:7402_1:N:0:GGCATTCT+CAAGCTAG ptg000092l 1 Processed 99000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1465:5499:11338_1:N:0:GGCATTCT+CAAGCTAG ptg000093l 1 Processed 100000000 sequence pairs so far Processed 101000000 sequence pairs so far Processed 102000000 sequence pairs so far Processed 103000000 sequence pairs so far Processed 104000000 sequence pairs so far Processed 105000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1484:24556:28946_1:N:0:GGCATTCT+CAAGCTAG ptg000069l 259768 Processed 106000000 sequence pairs so far Processed 107000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1491:26620:11422_1:N:0:GGCATTCT+CAAGCTAG ptg000082l 1 Processed 108000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1494:31589:22012_1:N:0:GGCATTCT+CAAGCTAG ptg000009l 19095963 Processed 109000000 sequence pairs so far Processed 110000000 sequence pairs so far Processed 111000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2107:48024:15722_1:N:0:GGCATTCT+CAAGCTAG ptg000033l 2625628 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2107:17031:25051_1:N:0:GGCATTCT+CAAGCTAG ptg000093l 1 Processed 112000000 sequence pairs so far Processed 113000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2117:29922:20975_1:N:0:GGCATTCT+CAAGCTAG ptg000149l 81124 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2118:16837:7682_1:N:0:GGCATTCT+CAAGCTAG ptg000033l 2625572 Processed 114000000 sequence pairs so far Processed 115000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2122:44091:15834_1:N:0:GGCATTCT+CAAGCTAG ptg000109l 39607 Processed 116000000 sequence pairs so far Processed 117000000 sequence pairs so far Processed 118000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2134:18528:27531_1:N:0:GGCATTCT+CAAGCTAG ptg000009l 19095961 Processed 119000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2140:44415:1434_1:N:0:GGCATTCT+CAAGCTAG ptg000069l 259768 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2141:36347:16381_1:N:0:GGCATTCT+CAAGCTAG ptg000033l 2625576 Processed 120000000 sequence pairs so far Processed 121000000 sequence pairs so far Processed 122000000 sequence pairs so far Processed 123000000 sequence pairs so far Processed 124000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2156:24751:17123_1:N:0:GGCATTCT+CAAGCTAG ptg000082l 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2157:23140:27559_1:N:0:GGCATTCT+CAAGCTAG ptg000117l 30001 Processed 125000000 sequence pairs so far Processed 126000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2166:30715:13747_1:N:0:GGCATTCT+CAAGCTAG ptg000033l 2625658 Processed 127000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2169:50848:11254_1:N:0:GGCATTCT+CAAGCTAG ptg000109l 39608 Processed 128000000 sequence pairs so far Processed 129000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2174:49537:12542_1:N:0:GGCATTCT+CAAGCTAG ptg000154l 34026 Processed 130000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2179:48283:28721_1:N:0:GGCATTCT+CAAGCTAG ptg000109l 39606 Processed 131000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2183:2554:17893_1:N:0:GGCATTCT+TAAGCTAG ptg000033l 2625659 Processed 132000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2186:37512:22852_1:N:0:GGCATTCT+CAAGCTAG ptg000009l 19095958 Processed 133000000 sequence pairs so far Processed 134000000 sequence pairs so far Processed 135000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2196:43678:23244_1:N:0:GGCATTCT+CAAGCTAG ptg000088l 1 Processed 136000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2201:32883:6099_1:N:0:GGCATTCT+CAAGCTAG ptg000033l 2625636 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2201:18075:10889_1:N:0:GGCATTCT+CAAGCTAG ptg000033l 2625656 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2201:13405:20877_1:N:0:GGCATTCT+CAAGCTAG ptg000109l 39608 Processed 137000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2205:28870:8844_1:N:0:GGCATTCT+CAAGCTAG ptg000056l 2 Processed 138000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2208:21344:17697_1:N:0:GGCATTCT+CAAGCTAG ptg000033l 2625578 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2209:46333:13775_1:N:0:GGCATTCT+CAAGCTAG ptg000033l 2625572 Processed 139000000 sequence pairs so far Processed 140000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2215:31087:22460_1:N:0:GGCATTCT+CAAGCTAG ptg000117l 30037 Processed 141000000 sequence pairs so far Processed 142000000 sequence pairs so far Processed 143000000 sequence pairs so far Processed 144000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2232:48639:8354_1:N:0:GGCATTCT+CAAGCTAG ptg000006l 3 Processed 145000000 sequence pairs so far Processed 146000000 sequence pairs so far Processed 147000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2242:42715:19280_1:N:0:GGCATTCT+CAAGCTAG ptg000109l 39662 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2244:35878:4082_1:N:0:GGCATTCT+CAAGCTAG ptg000033l 2625591 Processed 148000000 sequence pairs so far Processed 149000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2249:22412:22964_1:N:0:AGCATTCT+CAAGCTAG ptg000056l 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2250:47360:4460_1:N:0:GGCATTCT+CAAGCTAG ptg000008l 38432929 Processed 150000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2252:38143:27727_1:N:0:GGCATTCT+CAAGCTAG ptg000006l 1 Processed 151000000 sequence pairs so far Processed 152000000 sequence pairs so far Processed 153000000 sequence pairs so far Processed 154000000 sequence pairs so far Processed 155000000 sequence pairs so far Processed 156000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2276:26175:24995_1:N:0:GGCATTCT+CAAGCTAG ptg000009l 19095961 Processed 157000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2280:1777:3465_1:N:0:GGCATTCT+CAAGCTAG ptg000033l 2625573 Processed 158000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2284:20381:3059_1:N:0:GGCATTCT+CAAGCTAG ptg000109l 39600 Processed 159000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2288:35489:5875_1:N:0:GGCATTCT+CAAGCTAG ptg000092l 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2289:21692:9279_1:N:0:GGCATTCT+CAAGCTAG ptg000123l 44427 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2289:12442:17753_1:N:0:GGCATTCT+CAAGCTAG ptg000093l 1 Processed 160000000 sequence pairs so far Processed 161000000 sequence pairs so far Processed 162000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2304:27219:14924_1:N:0:GGCATTCT+CAAGCTAG ptg000061l 1 Processed 163000000 sequence pairs so far Processed 164000000 sequence pairs so far Processed 165000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2313:44860:3157_1:N:0:GGCATTCT+CAAGCTAG ptg000033l 2625636 Processed 166000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2320:39932:7430_1:N:0:GGCATTCT+CAAGCTAG ptg000093l 1 Processed 167000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2323:50185:23440_1:N:0:GGCATTCT+CAAGCTAG ptg000069l 259767 Processed 168000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2325:30650:2793_1:N:0:GGCATTCT+CAAGCTAG ptg000109l 39599 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2325:51123:28960_1:N:0:GGCATTCT+CAAGCTAG ptg000092l 1 Processed 169000000 sequence pairs so far Processed 170000000 sequence pairs so far Processed 171000000 sequence pairs so far Processed 172000000 sequence pairs so far Processed 173000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2344:42359:18608_1:N:0:GGCATTCT+CAAGCTAG ntLink_7 3 Processed 174000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2348:8340:28273_1:N:0:GGCATTCT+CAAGCTAG ptg000033l 2625613 Processed 175000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2353:39948:1434_1:N:0:GGCATTCT+CAAGCTAG ptg000109l 39608 Processed 176000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2355:40037:10805_1:N:0:GGCATTCT+CAAGCTAG ptg000033l 2625612 Processed 177000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2359:12531:27657_1:N:0:GGCATTCT+TAAGCTAG ptg000082l 1 Processed 178000000 sequence pairs so far Processed 179000000 sequence pairs so far Processed 180000000 sequence pairs so far Processed 181000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2374:6786:20149_1:N:0:GGCATTCT+CAAGCTAG ptg000026l 1 Processed 182000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2380:40741:9811_1:N:0:GGCATTCT+CAAGCTAG ptg000061l 1 Processed 183000000 sequence pairs so far Processed 184000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2385:7231:24561_1:N:0:GGCATTCT+CAAGCTAG ptg000080l 40077 Processed 185000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2388:16100:17921_1:N:0:GGCATTGT+CAAGCTAG ntLink_2 399336 Processed 186000000 sequence pairs so far Processed 187000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2401:25625:11464_1:N:0:GGCATTCT+CAAGCTAG ptg000093l 1 Processed 188000000 sequence pairs so far Processed 189000000 sequence pairs so far Processed 190000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2413:28271:21031_1:N:0:GGCATTCT+CAAGCTAG ptg000033l 2625627 Processed 191000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2418:50168:11954_1:N:0:GGCATTCT+CAAGCTAG ptg000033l 2625621 Processed 192000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2420:47199:5581_1:N:0:GGCATTCT+CAAGCTAG ptg000082l 2 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2420:46551:27125_1:N:0:GGCATTCT+CAAGCTAG ptg000033l 2625636 Processed 193000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2422:45969:21129_1:N:0:GGCATTCT+CAAGCTAG ptg000006l 3 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2425:29137:18636_1:N:0:GGCATTCT+CAAGCTAG ptg000033l 2625572 Processed 194000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2427:22606:15876_1:N:0:GGCATTCT+TAAGCTAG ptg000024l 2 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2427:25430:26424_1:N:0:GGCATTCT+CAAGCTAG ptg000033l 2625607 Processed 195000000 sequence pairs so far 213856184 reads; of these: 213856184 (100.00%) were paired; of these: 144404887 (67.52%) aligned concordantly 0 times 22338230 (10.45%) aligned concordantly exactly 1 time 47113067 (22.03%) aligned concordantly >1 times 32.48% overall alignment rate Processed 196000000 sequence pairs so far 213856184 reads; of these: 213856184 (100.00%) were paired; of these: 163144546 (76.29%) aligned concordantly 0 times 16548604 (7.74%) aligned concordantly exactly 1 time 34163034 (15.97%) aligned concordantly >1 times 23.71% overall alignment rate Processed 197000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2440:19766:3059_1:N:0:TGCATTCT+CAAGCTAG ptg000082l 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2441:34356:16493_1:N:0:TGCATTCT+CAAGCTAG ptg000009l 19095960 Processed 198000000 sequence pairs so far Processed 199000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2447:30100:12010_1:N:0:GGCATTCT+CAAGCTAG ptg000109l 39608 Processed 200000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2451:18358:20037_1:N:0:GGCATTCT+CAAGCTAG ptg000095l 1 Processed 201000000 sequence pairs so far Processed 202000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2458:9796:13425_1:N:0:GGCATTCT+CAAGCTAG ptg000069l 259785 Processed 203000000 sequence pairs so far Processed 204000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2467:26774:10875_1:N:0:GGCATTCT+CAAGCTAG ptg000093l 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2467:26782:10889_1:N:0:GGCATTCT+CAAGCTAG ptg000093l 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2467:26790:10904_1:N:0:GGCATTCT+CAAGCTAG ptg000093l 1 Processed 205000000 sequence pairs so far 213856184 reads; of these: 213856184 (100.00%) were paired; of these: 144402164 (67.52%) aligned concordantly 0 times 22317891 (10.44%) aligned concordantly exactly 1 time 47136129 (22.04%) aligned concordantly >1 times 32.48% overall alignment rate Processed 206000000 sequence pairs so far Processed 207000000 sequence pairs so far Processed 208000000 sequence pairs so far Processed 209000000 sequence pairs so far Processed 210000000 sequence pairs so far 213856184 reads; of these: 213856184 (100.00%) were paired; of these: 163139492 (76.28%) aligned concordantly 0 times 16507621 (7.72%) aligned concordantly exactly 1 time 34209071 (16.00%) aligned concordantly >1 times 23.72% overall alignment rate Processed 211000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2489:21158:27181_1:N:0:GGCATTCT+CAAGCTAG ptg000105l 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2490:30901:24071_1:N:0:AGCATTCT+CAAGCTAG ptg000109l 39590 Processed 212000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2493:36646:9363_1:N:0:GGCATTCT+CAAGCTAG ptg000144l 1 Processed 213000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2496:40320:19672_1:N:0:GGCATTCT+CAAGCTAG ptg000033l 2625577 Processed 213856184 sequences in total Successfully deleted the temporary files trimmed_ACR-173-TP2_S4_R1_001.fastq.gz_C_to_T.fastq, trimmed_ACR-173-TP2_S4_R1_001.fastq.gz_G_to_A.fastq, trimmed_ACR-173-TP2_S4_R2_001.fastq.gz_C_to_T.fastq and trimmed_ACR-173-TP2_S4_R2_001.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 213856184 Final Cytosine Methylation Report ================================= Total number of C's analysed: 4684212694 Total methylated C's in CpG context: 76855937 Total methylated C's in CHG context: 14470774 Total methylated C's in CHH context: 69704529 Total methylated C's in Unknown context: 12705187 Total unmethylated C's in CpG context: 734021072 Total unmethylated C's in CHG context: 855050390 Total unmethylated C's in CHH context: 2934109992 Total unmethylated C's in Unknown context: 48870104 C methylated in CpG context: 9.5% C methylated in CHG context: 1.7% C methylated in CHH context: 2.3% C methylated in unknown context (CN or CHN): 20.6% Bismark completed in 1d 8h 35m 35s ==================== Bismark run complete ====================