Bowtie 2 seems to be working fine (tested command '/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2 --version' [2.4.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/usr/bin/samtools' Reference genome folder provided is /home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/data/ (absolute path is '/home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/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 8 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/home/shared/8TB_HDD_03/sr320/github/timeseries_molecular/D-Apul/code'): /home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1A12_R1_001.fastp-trim.fq.gz /home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1A12_R2_001.fastp-trim.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Output will be written into the directory: /home/shared/8TB_HDD_03/sr320/github/timeseries_molecular/D-Apul/output/14-Apul-bismark/ Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-1.0 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /home/shared/8TB_HDD_03/sr320/github/timeseries_molecular/D-Apul/code Now reading in and storing sequence information of the genome specified in: /home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/data/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1A12_R1_001.fastp-trim.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1A12_R2_001.fastp-trim.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file 1A12_R1_001.fastp-trim.fq.gz to 1A12_R1_001.fastp-trim.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file 1A12_R1_001.fastp-trim.fq.gz (42093488 sequences in total) Writing a G -> A converted version of the input file 1A12_R2_001.fastp-trim.fq.gz to 1A12_R2_001.fastp-trim.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file 1A12_R2_001.fastp-trim.fq.gz (42093488 sequences in total) Input files are 1A12_R1_001.fastp-trim.fq.gz_C_to_T.fastq and 1A12_R2_001.fastp-trim.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/data/ with the specified options: -q --score-min L,0,-1.0 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from 1A12_R1_001.fastp-trim.fq.gz_C_to_T.fastq and 1A12_R2_001.fastp-trim.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.0 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:49926:1056_1:N:0:CCAGTATC+ATCTCGCT/1 99 ptg000031l_CT_converted 7909857 42 125M = 7909896 164 GTTATTAGTTAATTGTTAATTATTTTGAAATTAATTGTTAATTAAAGGTTGAAGGATAATAAGTGTATGTTAATTGTTTGATGATTAGTTTGTGTTTTTATTTTTGTTTATGGTGGTTAATTATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:92A32 YS:i:-12 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:49926:1056_2:N:0:CCAGTATC+ATCTCGCT/2 147 ptg000031l_CT_converted 7909896 42 125M = 7909857 -164 AATTAAAGGTTGAAGGATAATAAGTGTATGTTAATTGTTTGATGATTAGTTTGTGTTTTTATTTTTGTTTATGGTGGTTAATTATTAAAATGAATTAATTTTAGATGTTAATGTTAGAATAATGA IIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9 AS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:53A69T1 YS:i:-6 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1A12_R1_001.fastp-trim.fq.gz_C_to_T.fastq and 1A12_R2_001.fastp-trim.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.0 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00526:197:22KFKVLT4:3:1101:49926:1056_1:N:0:CCAGTATC+ATCTCGCT/1 77 * 0 0 * * 0 0 GTTATTAGTTAATTGTTAATTATTTTGAAATTAATTGTTAATTAAAGGTTGAAGGATAATAAGTGTATGTTAATTGTTTGATGATTAGTTTGTGTTTTTATTTTTGTTTATGGTGGTTAATTATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:49926:1056_2:N:0:CCAGTATC+ATCTCGCT/2 141 * 0 0 * * 0 0 TCATTATTCTAACATTAACATCTAAAATTAATTCATTTTAATAATTAACCACCATAAACAAAAATAAAAACACAAACTAATCATCAAACAATTAACATACACTTATTATCCTTCAACCTTTAATT 9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII YT:Z:UP >>> Writing bisulfite mapping results to 1A12_pe.bam <<< Reading in the sequence files /home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1A12_R1_001.fastp-trim.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1A12_R2_001.fastp-trim.fq.gz Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1159:39479:1490_1:N:0:CCAGTATC+ATCTCGCT ptg000096l 1 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1175:42003:26424_1:N:0:CCAGTATC+ATCTCGCT ptg000048l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1188:12183:26830_1:N:0:CCAGTATC+ATCTCGCT ptg000114l 51152 Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1209:38556:5076_1:N:0:CCAGTATC+ATCTCGCT ptg000004l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1225:4795:11352_1:N:0:CCAGTATC+ATCTCGCT ptg000127l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1225:32293:21914_1:N:0:CCAGTATC+ATCTCGCT ptg000116l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1229:46584:10147_1:N:0:CCAGTATC+ATCTCGCT ptg000025l 21443080 Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1286:16529:18440_1:N:0:CCAGTATC+ATCTCGCT ptg000095l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1288:4107:2933_1:N:0:CCAGTATC+ATCTCGCT ptg000046l 39598 Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1301:5548:8480_1:N:0:CCAGTATC+ATCTCGCT ptg000066l 66349 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1327:34534:4110_1:N:0:CCAGTATC+ATCTCGCT ptg000066l 2 Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1335:25657:27068_1:N:0:CCAGTATC+ATCTCGCT ptg000052l 52624 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1335:25681:27082_1:N:0:CCAGTATC+ATCTCGCT ptg000052l 52624 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1357:40506:2765_1:N:0:CCAGTATC+ATCTCGCT ptg000101l 1 Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1380:45896:27783_1:N:0:CCAGTATC+ATCTCGCT ptg000090l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1382:17905:6953_1:N:0:CCAGTATC+ATCTCGCT ptg000057l 1 Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1416:50921:18832_1:N:0:CCAGTATC+ATCTCGCT ptg000048l 76443 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1419:7530:7878_1:N:0:CCAGTATC+ATCTCGCT ptg000056l 59116 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1425:21239:19953_1:N:0:CCAGTATC+ATCTCGCT ntLink_7 182805 Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1460:21457:7976_1:N:0:CCAGTATC+ATCTCGCT ptg000121l 50741 Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1484:29752:17739_1:N:0:CCAGTATC+ATCTCGCT ptg000057l 1 Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2120:25746:10581_1:N:0:CCAGTATC+ATCTCGCT ptg000053l 71552 Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2154:18560:11254_1:N:0:CCAGTATC+ATCTCGCT ptg000066l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2173:26636:13467_1:N:0:CCAGTATC+ATCTCGCT ptg000117l 29997 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2173:26652:13467_1:N:0:CCAGTATC+ATCTCGCT ptg000117l 29997 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2175:4739:10581_1:N:0:CCAGTATC+ATCTCGCT ptg000048l 76446 Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2191:9408:10988_1:N:0:CCAGTATC+ATCTCGCT ptg000025l 21443080 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2191:9424:10988_1:N:0:CCAGTATC+ATCTCGCT ptg000025l 21443080 Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2251:4269:11730_1:N:0:CCAGTATC+ATCTCGCT ptg000144l 1 Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2281:19038:9559_1:N:0:CCAGTATC+ATCTCGCT ptg000125l 18901 Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2344:8930:9741_1:N:0:CCAGTATC+ATCTCGCT ntLink_7 182805 Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2368:40425:8984_1:N:0:CCAGTATC+ATCTCGCT ptg000011l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2406:35084:24001_1:N:0:CCAGTATC+ATCTCGCT ptg000039l 1139417 Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2410:41356:21241_1:N:0:CCAGTATC+ATCTCGCT ptg000129l 33365 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2413:39543:15778_1:N:0:CCAGTATC+ATCTCGCT ptg000054l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2413:39559:15778_1:N:0:CCAGTATC+ATCTCGCT ptg000054l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2413:39551:15792_1:N:0:CCAGTATC+ATCTCGCT ptg000054l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2427:3824:3395_1:N:0:CCAGTATC+ATCTCGCT ptg000056l 59095 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2427:3816:3409_1:N:0:CCAGTATC+ATCTCGCT ptg000056l 59095 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2436:42902:26326_1:N:0:CCAGTATC+ATCTCGCT ptg000094l 36817 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2436:42893:26340_1:N:0:CCAGTATC+ATCTCGCT ptg000094l 36817 Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2465:32713:8270_1:N:0:CCAGTATC+ATCTCGCT ptg000048l 1 Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1113:1696:19098_1:N:0:CCAGTATC+ATCTCGCT ptg000011l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1113:1704:19112_1:N:0:CCAGTATC+ATCTCGCT ptg000011l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1113:1720:19112_1:N:0:CCAGTATC+ATCTCGCT ptg000011l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1113:1712:19126_1:N:0:CCAGTATC+ATCTCGCT ptg000011l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1120:4132:2247_1:N:0:CCAGTATC+ATCTCGCT ptg000093l 36785 Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1144:19547:23188_1:N:0:CCAGTATC+ATCTCGCT ptg000048l 76439 Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1190:3832:3045_1:N:0:CCAGTATC+ATCTCGCT ptg000115l 1 Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1212:36315:5931_1:N:0:CCAGTATC+ATCTCGCT ptg000004l 15492348 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1216:8647:23258_1:N:0:CCAGTATC+ATCTCGCT ptg000121l 50750 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1224:12839:27909_1:N:0:CCAGTATC+ATCTCGCT ptg000082l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1224:12831:27923_1:N:0:CCAGTATC+ATCTCGCT ptg000082l 1 Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1234:45086:14840_1:N:0:CCAGTATC+ATCTCGCT ptg000006l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1237:36347:29604_1:N:0:CCAGTATC+ATCTCGCT ptg000137l 40575 Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1277:14894:22082_1:N:0:CCAGTATC+ATCTCGCT ptg000046l 39592 Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1305:17055:8256_1:N:0:CCAGTATC+ATCTCGCT ptg000097l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1319:4253:16409_1:N:0:CCAGTATC+ATCTCGCT ptg000113l 1 Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1336:42262:19196_1:N:0:CCAGTATC+ATCTCGCT ptg000090l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1349:15137:11912_1:N:0:CCAGTATC+ATCTCGCT ptg000025l 1 Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1373:3711:19812_1:N:0:CCAGTATC+ATCTCGCT ptg000097l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1384:49804:5945_1:N:0:CCAGTATC+ATCTCGCT ptg000048l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1391:2627:6309_1:N:0:CCAGTATC+ATCTCGCT ptg000121l 50750 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1391:14287:23496_1:N:0:CCAGTATC+ATCTCGCT ptg000083l 1 Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1411:9869:12318_1:N:0:CCAGTATC+ATCTCGCT ptg000160l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1416:10638:26144_1:N:0:CCAGTATC+ATCTCGCT ptg000123l 44473 Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1435:24686:23482_1:N:0:CCAGTATC+ATCTCGCT ptg000047l 2 Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1490:36800:22292_1:N:0:CCAGTATC+ATCTCGCT ptg000160l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1490:36792:22306_1:N:0:CCAGTATC+ATCTCGCT ptg000160l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1494:24767:22418_1:N:0:CCAGTATC+ATCTCGCT ptg000117l 1 Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2107:5726:4558_1:N:0:CCAGTATC+ATCTCGCT ptg000160l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2132:48016:17165_1:N:0:CCAGTATC+ATCTCGCT ptg000123l 44469 Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2169:15695:16577_1:N:0:CCAGTATC+ATCTCGCT ptg000115l 42075 Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2216:43395:27601_1:N:0:CCAGTATC+ATCTCGCT ptg000092l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2216:43387:27615_1:N:0:CCAGTATC+ATCTCGCT ptg000092l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2216:43403:27615_1:N:0:CCAGTATC+ATCTCGCT ptg000092l 2 Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2234:45386:5104_1:N:0:CCAGTATC+ATCTCGCT ptg000006l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2234:27518:16927_1:N:0:CCAGTATC+ATCTCGCT ptg000098l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2234:27534:16927_1:N:0:CCAGTATC+ATCTCGCT ptg000098l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2235:4989:23595_1:N:0:CCAGTATC+ATCTCGCT ptg000035l 10246563 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2261:12175:7570_1:N:0:CCAGTATC+ATCTCGCT ptg000117l 1 Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2292:37998:26606_1:N:0:CCAGTATC+ATCTCGCT ptg000113l 1 Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2444:15178:23861_1:N:0:CCAGTATC+ATCTCGCT ptg000115l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2446:12985:19224_1:N:0:CCAGTATC+ATCTCGCT ptg000108l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2447:38289:14504_1:N:0:CCAGTATC+ATCTCGCT ptg000012l 3 Processed 41000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2458:40992:11926_1:N:0:CCAGTATC+ATCTCGCT ptg000065l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2458:41008:11926_1:N:0:CCAGTATC+ATCTCGCT ptg000065l 1 Processed 42000000 sequence pairs so far 42093488 reads; of these: 42093488 (100.00%) were paired; of these: 15504298 (36.83%) aligned concordantly 0 times 8903783 (21.15%) aligned concordantly exactly 1 time 17685407 (42.01%) aligned concordantly >1 times 63.17% overall alignment rate 42093488 reads; of these: 42093488 (100.00%) were paired; of these: 15491292 (36.80%) aligned concordantly 0 times 8902530 (21.15%) aligned concordantly exactly 1 time 17699666 (42.05%) aligned concordantly >1 times 63.20% overall alignment rate Processed 42093488 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 168373952. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 168373952. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 168373952. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 168373952. Successfully deleted the temporary files 1A12_R1_001.fastp-trim.fq.gz_C_to_T.fastq and 1A12_R2_001.fastp-trim.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 42093488 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1281763961 Total methylated C's in CpG context: 19603054 Total methylated C's in CHG context: 1307618 Total methylated C's in CHH context: 5268058 Total methylated C's in Unknown context: 63391 Total unmethylated C's in CpG context: 179128297 Total unmethylated C's in CHG context: 216115676 Total unmethylated C's in CHH context: 860341258 Total unmethylated C's in Unknown context: 3126357 C methylated in CpG context: 9.9% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in unknown context (CN or CHN): 2.0% Bismark completed in 0d 2h 56m 18s ==================== Bismark run complete ====================