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 ../data/ (absolute path is '/home/shared/16TB_HDD_01/sr320/github/project-mytilus-methylation/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/16TB_HDD_01/sr320/github/project-mytilus-methylation/code'): ../data/271M_R1.fastp-trim.fq.gz ../data/271M_R2.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/16TB_HDD_01/sr320/github/project-mytilus-methylation/output/01.2-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/16TB_HDD_01/sr320/github/project-mytilus-methylation/code Now reading in and storing sequence information of the genome specified in: /home/shared/16TB_HDD_01/sr320/github/project-mytilus-methylation/data/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are ../data/271M_R1.fastp-trim.fq.gz and ../data/271M_R2.fastp-trim.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file 271M_R1.fastp-trim.fq.gz to 271M_R1.fastp-trim.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file 271M_R1.fastp-trim.fq.gz (90544317 sequences in total) Writing a G -> A converted version of the input file 271M_R2.fastp-trim.fq.gz to 271M_R2.fastp-trim.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file 271M_R2.fastp-trim.fq.gz (90544317 sequences in total) Input files are 271M_R1.fastp-trim.fq.gz_C_to_T.fastq and 271M_R2.fastp-trim.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /home/shared/16TB_HDD_01/sr320/github/project-mytilus-methylation/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 271M_R1.fastp-trim.fq.gz_C_to_T.fastq and 271M_R2.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: LH00469:254:22HGFVLT4:2:1101:1769:1014_1:N:0:CATACCAC+AACAACCG/1 99 NC_086377.1_CT_converted 2558138 2 131M = 2558272 265 AATTTTGGGATTTGTAATAGTTTTTTGTTTAGTGTGAGTTAAGGTTTTGTGTTGAAGGTTGTGAATTGATTTATATTTGTTTATTTTTATAAATTGTTATTTGGATGGAAAGTTGTTTAAATGATATTTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIII9II-IIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIII AS:i:-66 XS:i:-84 XN:i:0 XM:i:11 XO:i:0 XG:i:0 NM:i:11 MD:Z:13T1T21T25T11A1G29A0T0G8T4G7 YS:i:-24 YT:Z:CP LH00469:254:22HGFVLT4:2:1101:1769:1014_2:N:0:CATACCAC+AACAACCG/2 147 NC_086377.1_CT_converted 2558272 2 131M = 2558138 -265 ATATTTTTTTATATTTTTTTATTTTATTTATATATTTTTGTAGTAAAATTGTATTTATTAGAATAGTGTTGATTATGGGTATATGTTGTTTATATAGAGTATATAGATATGGAATGAATTAATATATATTG IIIIII99IIIIIIIIIIIIIIIIIIIIIIIIIIIII-III-IIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIII-I-II9IIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-24 XS:i:-30 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:73G24A12T0T18 YS:i:-66 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 271M_R1.fastp-trim.fq.gz_C_to_T.fastq and 271M_R2.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: LH00469:254:22HGFVLT4:2:1101:1769:1014_1:N:0:CATACCAC+AACAACCG/1 83 NC_086377.1_GA_converted 1468660 17 131M = 1468526 -265 ATAAATATCATTTAAACAACTTTCCATCCAAATAACAATTTATAAAAATAAACAAATATAAATCAATTCACAACCTTCAACACAAAACCTTAACTCACACTAAACAAAAAACTATTACAAATCCCAAAATT IIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIII-II9IIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XS:i:-62 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:109C21 YS:i:-12 YT:Z:CP LH00469:254:22HGFVLT4:2:1101:1769:1014_2:N:0:CATACCAC+AACAACCG/2 163 NC_086377.1_GA_converted 1468526 17 131M = 1468660 265 CAATATATATTAATTCATTCCATATCTATATACTCTATATAAACAACATATACCCATAATCAACACTATTCTAATAAATACAATTTTACTACAAAAATATATAAATAAAATAAAAAAATATAAAAAAATAT IIIIIIIIIIIIIIIIIIIIIIIIIII9II-I-IIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIII-III-IIIIIIIIIIIIIIIIIIIIIIIIIIIII99IIIIII AS:i:-12 XS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:32T43C54 YS:i:-6 YT:Z:CP >>> Writing bisulfite mapping results to 271M_pe.bam <<< Reading in the sequence files ../data/271M_R1.fastp-trim.fq.gz and ../data/271M_R2.fastp-trim.fq.gz Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1109:10767:4460_1:N:0:CATACCAC+AACAACCG NW_026963384.1 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 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1144:25026:23903_1:N:0:CATACCAC+AACAACCG NW_026963814.1 1 Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1158:3711:17375_1:N:0:CATACCAC+AACAACCG NW_026963647.1 17436 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1159:32624:13019_1:N:0:CATACCAC+AACAACCG NW_026963811.1 1 Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1174:4658:15036_1:N:0:TATACCAC+AACAACCG NW_026963307.1 1 Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1187:12548:18216_1:N:0:CATACCAC+AACAACCG NC_086381.1 1 Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1202:21061:28301_1:N:0:CATACCAC+AACAACCG NW_026963754.1 1 Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1212:9246:3507_1:N:0:CATACCAC+AACAACCG NW_026963514.1 23967 Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1234:24071:20289_1:N:0:CATACCAC+AACAACCG NW_026963293.1 499871 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1234:24063:20303_1:N:0:CATACCAC+AACAACCG NW_026963293.1 499871 Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1240:10290:16268_1:N:0:CATACCAC+AACAACCG NW_026963434.1 1 Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1248:27769:23861_1:N:0:CATACCAC+AACAACCG NW_026963335.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1253:16367:14966_1:N:0:CATACCAC+AACAACCG NW_026963730.1 1 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 LH00469:254:22HGFVLT4:2:1286:47458:22474_1:N:0:CATACCAC+AACAACCG NW_026963756.1 2 Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1301:7045:27545_1:N:0:CATACCAC+AACAACCG NW_026963804.1 2 Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1318:47595:27082_1:N:0:CATACCAC+AACAACCG NW_026963415.1 3 Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1342:5645:9629_1:N:0:CATACCAC+AACAACCG NW_026963581.1 3 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 LH00469:254:22HGFVLT4:2:1374:13033:11408_1:N:0:CATACCAC+AACAACCG NW_026963307.1 124895 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1374:13041:11422_1:N:0:CATACCAC+AACAACCG NW_026963307.1 124895 Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1381:27996:25738_1:N:0:CATACCAC+AACAACCG NW_026963669.1 58930 Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1387:45014:23679_1:N:0:CATACCAC+AACAACCG NW_026963347.1 1227520 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1395:40369:22950_1:N:0:CATACCAC+AACAACCG NW_026963508.1 37046 Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1408:18843:2919_1:N:0:CATACCAC+AACAACCG NW_026963404.1 1 Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1416:37577:13383_1:N:0:CATACCAC+AACAACCG NW_026963326.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1417:40668:16353_1:N:0:CATACCAC+AACAACCG NW_026963684.1 18534 Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1424:6567:15260_1:N:0:CATACCAC+AACAACCG NW_026963588.1 1 Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1434:14360:13649_1:N:0:CATACCAC+AACAACCG NW_026963494.1 1 Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1443:3274:24239_1:N:0:CATACCAC+AACAACCG NW_026963415.1 1 Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1453:49820:17067_1:N:0:CATACCAC+AACAACCG NW_026963554.1 23176 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1455:7158:17375_1:N:0:CATACCAC+AACAACCG NW_026963669.1 58933 Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1467:34769:21521_1:N:0:CATACCAC+AACAACCG NW_026963559.1 1 Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1488:3088:23076_1:N:0:CATACCAC+AACAACCG NW_026963415.1 3 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1488:3104:23076_1:N:0:CATACCAC+AACAACCG NW_026963415.1 3 Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2108:44269:6617_1:N:0:CATACCAC+AACAACCG NW_026963340.1 4220815 Processed 38000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2121:28044:8004_1:N:0:CATACCAC+AACAACCG NW_026963636.1 18740 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2121:15202:12192_1:N:0:CATACCAC+AACAACCG NW_026963442.1 1 Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2132:31492:24309_1:N:0:CATACCAC+AACAACCG NW_026963628.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2132:16586:27475_1:N:0:CATACCAC+AACAACCG NW_026963725.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2134:20575:26200_1:N:0:CATACCAC+AACAACCG NW_026963308.1 1 Processed 41000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2149:3096:12556_1:N:0:CATACCAC+AACAACCG NW_026963575.1 31997 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2150:46940:22838_1:N:0:CATACCAC+AACAACCG NW_026963377.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2150:46956:22838_1:N:0:CATACCAC+AACAACCG NW_026963377.1 2 Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2165:29905:23805_1:N:0:CATACCAC+AACAACCG NW_026963777.1 18501 Processed 44000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2179:42052:28441_1:N:0:CATACCAC+AACAACCG NW_026963504.1 2 Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2203:34947:17179_1:N:0:CATACCAC+AACAACCG NW_026963603.1 20012 Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2226:9780:26760_1:N:0:CATACCAC+AACAACCG NW_026963494.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2226:9812:26760_1:N:0:CATACCAC+AACAACCG NW_026963494.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2233:25479:25948_1:N:0:CATACCAC+AACAACCG NW_026963456.1 2 Processed 49000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2234:3525:26886_1:N:0:CATACCAC+AACAACCG NW_026963581.1 3 Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2323:1162:5847_1:N:0:CATACCAC+NACAACCG NW_026963340.1 4220807 Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2352:41599:13061_1:N:0:CATACCAC+AACAACCG NW_026963684.1 18465 Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 63000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2398:50120:4922_1:N:0:CATACCAC+AACAACCG NW_026963347.1 1227499 Processed 64000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2423:41688:20695_1:N:0:CATACCAC+AACAACCG NW_026963603.1 20039 Processed 65000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2424:20794:19939_1:N:0:CATACCAC+AACAACCG NW_026963293.1 499905 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2424:20810:19939_1:N:0:CATACCAC+AACAACCG NW_026963293.1 499905 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2430:32592:24085_1:N:0:CATACCAC+AACAACCG NW_026963789.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2432:4989:23651_1:N:0:CATACCAC+AACAACCG NW_026963568.1 1 Processed 66000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2438:22323:16815_1:N:0:CATACCAC+AACAACCG NW_026963352.1 336904 Processed 67000000 sequence pairs so far Processed 68000000 sequence pairs so far Processed 69000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2481:45799:19770_1:N:0:CATACCAC+AACAACCG NW_026963808.1 3 Processed 70000000 sequence pairs so far Processed 71000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2496:11051:7640_1:N:0:CATACCAC+AACAACCG NW_026963443.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2496:11067:7640_1:N:0:CATACCAC+AACAACCG NW_026963443.1 1 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1101:18819:25570_1:N:0:CATACCAC+AACAACCG NW_026963744.1 1 Processed 72000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1129:35182:7332_1:N:0:CATACCAC+AACAACCG NW_026963456.1 1 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1149:15218:11408_1:N:0:CATACCAC+AACAACCG NW_026963502.1 2 Processed 73000000 sequence pairs so far Processed 74000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1212:13486:8298_1:N:0:CATACCAC+AACAACCG NW_026963789.1 1 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1236:42125:19686_1:N:0:CATACCAC+AACAACCG NW_026963712.1 21918 Processed 75000000 sequence pairs so far Processed 76000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1291:7490:20667_1:N:0:CATACCAC+AACAACCG NC_086377.1 88128948 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1310:26474:14504_1:N:0:CATACCAC+AACAACCG NW_026963400.1 2 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1321:22906:8102_1:N:0:CATACCAC+AACAACCG NW_026963361.1 3 Processed 77000000 sequence pairs so far 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 LH00586:122:22HTFTLT4:7:1459:38783:12472_1:N:0:CATACCAC+AACAACCG NW_026963415.1 2 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1465:25568:17641_1:N:0:CATACCAC+AACAACCG NW_026963725.1 2 Processed 81000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1488:23343:5384_1:N:0:CATACCAC+AACAACCG NW_026963415.1 1 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2104:42327:6001_1:N:0:CATACCAC+AACAACCG NW_026963724.1 1 Processed 82000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2140:31063:28918_1:N:0:CATACCAC+AACAACCG NW_026963293.1 499882 Processed 83000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2173:1623:25360_1:N:0:CATACCAC+AACAACCG NW_026963361.1 3 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2191:38847:8914_1:N:0:CATACCAC+AACAACCG NW_026963415.1 1 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2218:45920:9167_1:N:0:CATACCAC+AACAACCG NW_026963361.1 1 Processed 84000000 sequence pairs so far Processed 85000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2274:2359:14195_1:N:0:CATACCAC+AACAACCG NW_026963749.1 2 Processed 86000000 sequence pairs so far Processed 87000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2375:21222:4936_1:N:0:CATACCAC+AACAACCG NW_026963812.1 1 Processed 88000000 sequence pairs so far Processed 89000000 sequence pairs so far Processed 90000000 sequence pairs so far 90544317 reads; of these: 90544317 (100.00%) were paired; of these: 39308584 (43.41%) aligned concordantly 0 times 17819117 (19.68%) aligned concordantly exactly 1 time 33416616 (36.91%) aligned concordantly >1 times 56.59% overall alignment rate 90544317 reads; of these: 90544317 (100.00%) were paired; of these: 39300621 (43.40%) aligned concordantly 0 times 17824650 (19.69%) aligned concordantly exactly 1 time 33419046 (36.91%) aligned concordantly >1 times 56.60% overall alignment rate Processed 90544317 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 362177268. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 362177268. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 362177268. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 362177268. Successfully deleted the temporary files 271M_R1.fastp-trim.fq.gz_C_to_T.fastq and 271M_R2.fastp-trim.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 90544317 Final Cytosine Methylation Report ================================= Total number of C's analysed: 2185930207 Total methylated C's in CpG context: 28991604 Total methylated C's in CHG context: 3372079 Total methylated C's in CHH context: 15852510 Total methylated C's in Unknown context: 413774 Total unmethylated C's in CpG context: 224805597 Total unmethylated C's in CHG context: 347169431 Total unmethylated C's in CHH context: 1565738986 Total unmethylated C's in Unknown context: 12212394 C methylated in CpG context: 11.4% C methylated in CHG context: 1.0% C methylated in CHH context: 1.0% C methylated in unknown context (CN or CHN): 3.3% Bismark completed in 0d 6h 15m 45s ==================== Bismark run complete ==================== Unable to flush stdout: Broken pipe