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/1H6_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/1H6_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/1H6_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/1H6_R2_001.fastp-trim.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file 1H6_R1_001.fastp-trim.fq.gz to 1H6_R1_001.fastp-trim.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file 1H6_R1_001.fastp-trim.fq.gz (38893195 sequences in total) Writing a G -> A converted version of the input file 1H6_R2_001.fastp-trim.fq.gz to 1H6_R2_001.fastp-trim.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file 1H6_R2_001.fastp-trim.fq.gz (38893195 sequences in total) Input files are 1H6_R1_001.fastp-trim.fq.gz_C_to_T.fastq and 1H6_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 1H6_R1_001.fastp-trim.fq.gz_C_to_T.fastq and 1H6_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: LH00526:197:22KFKVLT4:3:1101:38831:1070_1:N:0:CACGCAAT+ATGGAAGG/1 99 ptg000020l_CT_converted 10105059 7 125M = 10105069 135 TAAGGTTATTTTGAAAATTTGTTTTTAGGGAGGTAGGAAATTTGGGTTATGAATTTTTTATAAGTTTGAGAAATTGTGGATTTTGTTTTTATTTTTTATTATTAAGTAGGGTTTTTATAGATAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-30 XS:i:-48 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:14G44T6A36T12G8 YS:i:-42 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:38831:1070_2:N:0:CACGCAAT+ATGGAAGG/2 147 ptg000020l_CT_converted 10105069 7 125M = 10105059 -135 TTGAAAATTTGTTTTTAGGGAGGTAGGAAATTTGGGTTATGAATTTTTTATAAGTTTGAGAAATTGTGGATTTTGTTTTTATTTTTTATTATTAAGTAGGGTTTTTATAGATAATTTTTGAATTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-42 XS:i:-60 XN:i:0 XM:i:7 XO:i:0 XG:i:0 NM:i:7 MD:Z:4G44T6A36T12G14G1G1 YS:i:-30 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1H6_R1_001.fastp-trim.fq.gz_C_to_T.fastq and 1H6_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: LH00526:197:22KFKVLT4:3:1101:38831:1070_1:N:0:CACGCAAT+ATGGAAGG/1 83 ptg000036l_GA_converted 2203578 17 125M = 2203568 -135 ATTATCTATAAAAACCCTACTTAATAATAAAAAATAAAAACAAAATCCACAATTTCTCAAACTTATAAAAAATTCATAACCCAAATTTCCTACCTCCCTAAAAACAAATTTTCAAAATAACCTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:-30 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:-6 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:38831:1070_2:N:0:CACGCAAT+ATGGAAGG/2 163 ptg000036l_GA_converted 2203568 17 125M = 2203578 135 CAATTCAAAAATTATCTATAAAAACCCTACTTAATAATAAAAAATAAAAACAAAATCCACAATTTCTCAAACTTATAAAAAATTCATAACCCAAATTTCCTACCTCCCTAAAAACAAATTTTCAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XS:i:-42 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:1C123 YS:i:0 YT:Z:CP >>> Writing bisulfite mapping results to 1H6_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/1H6_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/1H6_R2_001.fastp-trim.fq.gz Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1126:1785:5412_1:N:0:CACGCAAT+ATGGAAGG ptg000118l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1126:1801:5412_1:N:0:CACGCAAT+ATGGAAGG ptg000118l 1 Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1149:18366:10693_1:N:0:CACGCAAT+ATGGAAGG ptg000057l 39951 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1150:36363:26886_1:N:0:CACGCAAT+ATGGAAGG ptg000065l 49688 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1150:36355:26900_1:N:0:CACGCAAT+ATGGAAGG ptg000065l 49688 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1176:43638:2527_1:N:0:CACGCAAT+ATGGAAGG ptg000127l 27812 Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1208:28627:9068_1:N:0:CACGCAAT+ATGGAAGG ntLink_7 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1226:27000:8466_1:N:0:CACGCAAT+ATGGAAGG ptg000092l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1237:25778:22544_1:N:0:CACGCAAT+ATGGAAGG ptg000113l 1 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1250:10290:1784_1:N:0:CACGCAAT+ATGGAAGG ptg000113l 1 Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1323:48073:17963_1:N:0:CACGCAAT+ATGGAAGG ptg000047l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1323:48089:17963_1:N:0:CACGCAAT+ATGGAAGG ptg000047l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1330:20365:7261_1:N:0:CACGCAAT+ATGGAAGG ptg000185l 34510 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1336:40401:13089_1:N:0:CACGCAAT+ATGGAAGG ntLink_2 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1338:28101:1210_1:N:0:CACGCAAT+ATGGAAGG ptg000169l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1340:22339:24967_1:N:0:CACGCAAT+ATGGAAGG ptg000075l 1 Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1358:3517:16451_1:N:0:CACGCAAT+ATGGAAGG ptg000116l 48503 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1361:13041:9881_1:N:0:CACGCAAT+ATGGAAGG ptg000113l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1361:13049:9895_1:N:0:CACGCAAT+ATGGAAGG ptg000113l 1 Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1407:47668:19084_1:N:0:CACGCAAT+ATGGAAGG ptg000011l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1413:1534:2961_1:N:0:CACGCAAT+ATGGAAGG ptg000007l 12295855 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1413:1542:2975_1:N:0:CACGCAAT+ATGGAAGG ptg000007l 12295855 Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1437:32034:18944_1:N:0:CACGCAAT+ATGGAAGG ptg000094l 36804 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1440:44115:6687_1:N:0:CACGCAAT+ATGGAAGG ptg000122l 1 Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1466:23812:28974_1:N:0:CACGCAAT+ATGGAAGG ptg000131l 1 Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2109:43889:9012_1:N:0:CACGCAAT+ATGGAAGG ptg000046l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2116:45742:28189_1:N:0:CACGCAAT+ATGGAAGG ptg000024l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2117:20802:4068_1:N:0:CACGCAAT+ATGGAAGG ptg000107l 62638 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2117:7231:7836_1:N:0:CACGCAAT+ATGGAAGG ptg000050l 26307 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2128:8631:11240_1:N:0:CACGCAAT+ATGGAAGG ptg000096l 1 Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2146:31160:28805_1:N:0:CACGCAAT+ATGGAAGG ptg000133l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2156:24872:8564_1:N:0:CACGCAAT+ATGGAAGG ptg000089l 46435 Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2190:31548:12472_1:N:0:CACGCAAT+ATGGAAGG ptg000129l 33365 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2210:15671:16927_1:N:0:CACGCAAT+ATGGAAGG ptg000047l 2 Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2248:29250:17851_1:N:0:CACGCAAT+ATGGAAGG ptg000096l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2257:42141:2009_1:N:0:CACGCAAT+ATGGAAGG ptg000067l 2 Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2293:23302:11982_1:N:0:CACGCAAT+ATGGAAGG ptg000121l 50750 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2310:19191:15008_1:N:0:CACGCAAT+ATGGAAGG ptg000121l 50744 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2310:19208:15008_1:N:0:CACGCAAT+ATGGAAGG ptg000121l 50744 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2310:19216:15022_1:N:0:CACGCAAT+ATGGAAGG ptg000121l 50744 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2329:29638:11016_1:N:0:CACGCAAT+ATGGAAGG ptg000112l 2 Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2361:38370:16521_1:N:0:CACGCAAT+ATGGAAGG ptg000130l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2361:38362:16535_1:N:0:CACGCAAT+ATGGAAGG ptg000130l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2366:27292:27629_1:N:0:CACGCAAT+ATGGAAGG ptg000129l 33355 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2366:27300:27643_1:N:0:CACGCAAT+ATGGAAGG ptg000129l 33355 Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2402:26604:26942_1:N:0:CACGCAAT+ATGGAAGG ptg000123l 44476 Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2445:51916:8620_1:N:0:CACGCAAT+ATGGAAGG ptg000106l 40378 Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2477:35958:9012_1:N:0:CACGCAAT+ATGGAAGG ptg000045l 57990 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2494:46389:16843_1:N:0:CACGCAAT+ATGGAAGG ptg000089l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1111:46454:29366_1:N:0:CACGCAAT+ATGGAAGG ntLink_0 1 Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1130:46883:2457_1:N:0:CACGCAAT+ATGGAAGG ptg000025l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1130:46915:2457_1:N:0:CACGCAAT+ATGGAAGG ptg000025l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1130:46907:2471_1:N:0:CACGCAAT+ATGGAAGG ptg000025l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1135:2983:4152_1:N:0:CACGCAAT+ATGGAAGG ptg000048l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1143:25115:22852_1:N:0:CACGCAAT+ATGGAAGG ptg000009l 19095997 Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1159:4083:29170_1:N:0:CACGCAAT+ATGGAAGG ptg000025l 21443080 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1168:7360:18398_1:N:0:CACGCAAT+ATGGAAGG ptg000137l 40587 Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1229:27737:20947_1:N:0:CACGCAAT+ATGGAAGG ptg000018l 3 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1230:24289:22600_1:N:0:CACGCAAT+ATGGAAGG ptg000092l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1244:46195:9391_1:N:0:CACGCAAT+ATGGAAGG ptg000121l 50738 Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1270:22250:14560_1:N:0:CACGCAAT+ATGGAAGG ntLink_0 96482 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1291:6219:28385_1:N:0:CACGCAAT+ATGGAAGG ptg000127l 27816 Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1302:36072:16801_1:N:0:CACGCAAT+ATGGAAGG ptg000096l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1304:50694:12360_1:N:0:CACGCAAT+ATGGAAGG ptg000092l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1313:34728:13075_1:N:0:CACGCAAT+ATGGAAGG ptg000128l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1316:20284:9307_1:N:0:CACGCAAT+ATGGAAGG ptg000106l 40380 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1317:11310:24589_1:N:0:CACGCAAT+ATGGAAGG ptg000129l 1 Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1376:38766:25023_1:N:0:CACGCAAT+ATGGAAGG ptg000095l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1384:36541:28203_1:N:0:CACGCAAT+ATGGAAGG ptg000113l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1390:18390:22810_1:N:0:CACGCAAT+ATGGAAGG ptg000066l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1395:21878:7612_1:N:0:CACGCAAT+ATGGAAGG ptg000118l 1 Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1426:34235:17011_1:N:0:CACGCAAT+ATGGAAGG ptg000174l 27224 Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1451:30019:23020_1:N:0:CACGCAAT+ATGGAAGG ptg000046l 39587 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1464:27648:7121_1:N:0:CACGCAAT+ATGGAAGG ptg000158l 12822 Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1498:33167:3031_1:N:0:CACGCAAT+ATGGAAGG ptg000118l 2 Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2123:7660:16759_1:N:0:CACGCAAT+ATGGAAGG ptg000020l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2123:7676:16759_1:N:0:CACGCAAT+ATGGAAGG ptg000020l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2133:25884:11324_1:N:0:CACGCAAT+ATGGAAGG ptg000096l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2146:20033:22992_1:N:0:CACGCAAT+ATGGAAGG ptg000114l 51152 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2150:31977:27867_1:N:0:CACGCAAT+ATGGAAGG ptg000128l 44518 Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2178:43816:23314_1:N:0:CACGCAAT+ATGGAAGG ptg000045l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2187:29727:18258_1:N:0:CACGCAAT+ATGGAAGG ptg000098l 55096 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2203:18236:1868_1:N:0:CACGCAAT+ATGGAAGG ptg000006l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2210:8663:7906_1:N:0:CACGCAAT+ATGGAAGG ptg000096l 1 Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2221:21757:20569_1:N:0:CACGCAAT+ATGGAAGG ptg000105l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2230:29331:6869_1:N:0:CACGCAAT+ATGGAAGG ptg000095l 40237 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2244:11617:15904_1:N:0:CACGCAAT+ATGGAAGG ptg000130l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2257:6098:16493_1:N:0:CACGCAAT+ATGGAAGG ptg000046l 2 Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2285:40450:11464_1:N:0:CACGCAAT+ATGGAAGG ptg000109l 39600 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2292:20349:4544_1:N:0:CACGCAAT+ATGGAAGG ptg000048l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2293:3889:17123_1:N:0:CACGCAAT+ATGGAAGG ptg000083l 2 Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2331:37099:25780_1:N:0:CACGCAAT+ATGGAAGG ptg000066l 66351 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2336:11989:17641_1:N:0:CACGCAAT+ATGGAAGG ptg000116l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2338:28805:2681_1:N:0:CACGCAAT+ATGGAAGG ptg000039l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2338:33547:29044_1:N:0:CACGCAAT+ATGGAAGG ptg000124l 54832 Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2366:8469:13481_1:N:0:CACGCAAT+ATGGAAGG ptg000006l 3 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2375:51309:25304_1:N:0:CACGCAAT+ATGGAAGG ptg000002l 1 Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2445:19208:8928_1:N:0:CACGCAAT+ATGGAAGG ptg000006l 2 Processed 38000000 sequence pairs so far 3889319538893195 reads; of these: reads; of these: 3889319538893195 ( (100.00100.00%%) were paired; of these:) were paired; of these: 1684416316863853 ( (43.3143.36%%) aligned concordantly 0 times) aligned concordantly 0 times 74172637410367 ( (19.0719.05%%) aligned concordantly exactly 1 time) aligned concordantly exactly 1 time 1463176914618975 ( (37.6237.59%%) aligned concordantly >1 times) aligned concordantly >1 times 56.6956.64%% overall alignment rate overall alignment rate Processed 38893195 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 155572780. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 155572780. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 155572780. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 155572780. Successfully deleted the temporary files 1H6_R1_001.fastp-trim.fq.gz_C_to_T.fastq and 1H6_R2_001.fastp-trim.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 38893195 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1068786104 Total methylated C's in CpG context: 20062939 Total methylated C's in CHG context: 1171969 Total methylated C's in CHH context: 4789925 Total methylated C's in Unknown context: 59891 Total unmethylated C's in CpG context: 144809117 Total unmethylated C's in CHG context: 178685961 Total unmethylated C's in CHH context: 719266193 Total unmethylated C's in Unknown context: 2652452 C methylated in CpG context: 12.2% C methylated in CHG context: 0.7% C methylated in CHH context: 0.7% C methylated in unknown context (CN or CHN): 2.2% Bismark completed in 0d 2h 32m 8s ==================== Bismark run complete ====================