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/72M_R1.fastp-trim.fq.gz ../data/72M_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/72M_R1.fastp-trim.fq.gz and ../data/72M_R2.fastp-trim.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file 72M_R1.fastp-trim.fq.gz to 72M_R1.fastp-trim.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file 72M_R1.fastp-trim.fq.gz (91280527 sequences in total) Writing a G -> A converted version of the input file 72M_R2.fastp-trim.fq.gz to 72M_R2.fastp-trim.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file 72M_R2.fastp-trim.fq.gz (91280527 sequences in total) Input files are 72M_R1.fastp-trim.fq.gz_C_to_T.fastq and 72M_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 72M_R1.fastp-trim.fq.gz_C_to_T.fastq and 72M_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: LH00469:254:22HGFVLT4:2:1101:3128:1014_1:N:0:CAACACCT+AGCTACCA/1 99 NC_086375.1_CT_converted 24177712 6 126M = 24177694 -144 ATGTTGGGGTGTGTTATTTTATTTGTATGTTTTGTATTTGATAGTTGTATTATTAAATGGTGTATTTTATAGGATTTTGTTATGTATATGGGTTATAATTATAGGGTTAGATTGTTTTTTTTTTTT IIIII9IIIIIIIIIII9II-IIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-30 XS:i:-36 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:44G38A36A2G1G0 YS:i:-23 YT:Z:CP LH00469:254:22HGFVLT4:2:1101:3128:1014_2:N:0:CAACACCT+AGCTACCA/2 147 NC_086375.1_CT_converted 24177694 6 9M2I115M = 24177712 144 TTATGGATTTGTGTGATATTATGTTGGGGTGTGTTATTTTATTTGTATGTTTTGTATTTGATAGTTGTATTATTAAATGGTGTATTTTATAGGATTTTGTTATGTATATGGGTTATAATTATAGGG 9IIIIIIIIIIIIIIIIIIIII9IIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII9IIIIIIIIIIIIIIIIIIIIIIIII AS:i:-23 XS:i:-29 XN:i:0 XM:i:2 XO:i:1 XG:i:2 NM:i:4 MD:Z:62G38A22 YS:i:-30 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 72M_R1.fastp-trim.fq.gz_C_to_T.fastq and 72M_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: LH00469:254:22HGFVLT4:2:1101:3128:1014_1:N:0:CAACACCT+AGCTACCA/1 83 NC_086385.1_GA_converted 49520160 2 126M = 49520180 144 AAAAAAAAAAAACAATCTAACCCTATAATTATAACCCATATACATAACAAAATCCTATAAAATACACCATTTAATAATACAACTATCAAATACAAAACATACAAATAAAATAACACACCCCAACAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIII-II9IIIIIIIIIII9IIIII AS:i:-48 XS:i:-60 XN:i:0 XM:i:8 XO:i:0 XG:i:0 NM:i:8 MD:Z:0C1C2T36T7T11A8C9C44 YS:i:-41 YT:Z:CP LH00469:254:22HGFVLT4:2:1101:3128:1014_2:N:0:CAACACCT+AGCTACCA/2 163 NC_086385.1_GA_converted 49520180 2 111M2I13M = 49520160 -144 CCCTATAATTATAACCCATATACATAACAAAATCCTATAAAATACACCATTTAATAATACAACTATCAAATACAAAACATACAAATAAAATAACACACCCCAACATAATATCACACAAATCCATAA IIIIIIIIIIIIIIIIIIIIIIIII9IIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIII9IIIIIIIIIIIIIIIIIIIII9 AS:i:-41 XS:i:-53 XN:i:0 XM:i:5 XO:i:1 XG:i:2 NM:i:7 MD:Z:22T7T11A8C9C62 YS:i:-48 YT:Z:CP >>> Writing bisulfite mapping results to 72M_pe.bam <<< Reading in the sequence files ../data/72M_R1.fastp-trim.fq.gz and ../data/72M_R2.fastp-trim.fq.gz Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1101:17994:19182_1:N:0:CAACACCT+AGCTACCA NW_026963443.1 56333 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1101:18002:19196_1:N:0:CAACACCT+AGCTACCA NW_026963443.1 56333 Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1110:18528:15848_1:N:0:CAACACCT+AGCTACCA NW_026963443.1 1 Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1135:42966:7163_1:N:0:CAACACCT+AGCTACCA NW_026963415.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1137:13543:5426_1:N:0:CAACACCT+AGCTACCA NW_026963634.1 21065 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1138:21870:7402_1:N:0:CAACACCT+AGCTACCA NW_026963454.1 1 Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1148:14822:21872_1:N:0:CAACACCT+AGCTCCCA NW_026963721.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1148:14822:21900_1:N:0:CAACACCT+AGCTACCA NW_026963721.1 1 Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1168:5572:5412_1:N:0:CAACACCT+AGCTACCA NW_026963299.1 2 Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1183:35570:28147_1:N:0:CAACACCT+AGCTACCA NW_026963378.1 1 Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1187:31451:1714_1:N:0:CAACACCT+AGCTACCA NW_026963642.1 22044 Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1204:41048:23735_1:N:0:CAACACCT+AGCTACCA NW_026963711.1 2 Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1228:30585:17753_1:N:0:CAACACCT+AGCTACCA NW_026963765.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1228:30577:17767_1:N:0:CAACACCT+AGCTACCA NW_026963765.1 2 Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1233:45281:24113_1:N:0:CAACACCT+AGCTACCA NW_026963415.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1234:26571:1224_1:N:0:CAACACCT+AGCTACCA NW_026963771.1 24026 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 LH00469:254:22HGFVLT4:2:1261:15412:6701_1:N:0:CAACACCT+AGCTACCA NW_026963675.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1265:47789:22964_1:N:0:CAACACCT+AGCTACCA NW_026963414.1 35637 Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1302:15817:2247_1:N:0:CAACACCT+AGCTACCA NW_026963685.1 25569 Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1315:40498:7430_1:N:0:CAACACCT+AGCTACCA NW_026963496.1 27405 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1318:5046:25402_1:N:0:CAACACCT+AGCTACCA NW_026963407.1 2 Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1325:43525:4264_1:N:0:CAACACCT+AGCTACCA NW_026963604.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1325:8631:15442_1:N:0:CAACACCT+AGCTACCA NW_026963415.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1325:8647:15442_1:N:0:CAACACCT+AGCTACCA NW_026963415.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1325:8655:15456_1:N:0:CAACACCT+AGCTACCA NW_026963415.1 2 Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1335:42076:25261_1:N:0:CAACACCT+AGCTACCA NW_026963446.1 2 Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1350:17354:6393_1:N:0:CAACACCT+AGCTACCA NW_026963621.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1350:49909:15988_1:N:0:CAACACCT+AGCTACCA NW_026963791.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1357:37326:25976_1:N:0:CAACACCT+AGCTACCA NW_026963734.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1357:37318:25990_1:N:0:CAACACCT+AGCTACCA NW_026963734.1 2 Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1378:43687:8634_1:N:0:CAACACCT+AGCTACCA NW_026963415.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1382:2683:4642_1:N:0:CAACACCT+AGCTACCA NW_026963745.1 20566 Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1395:35643:6841_1:N:0:CAACACCT+AGCTACCA NW_026963574.1 19306 Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1414:36355:9307_1:N:0:CAACACCT+AGCTACCA NW_026963415.1 2 Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1426:50007:12094_1:N:0:CAACACCT+AGCTACCA NW_026963705.1 2 Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1430:52127:13383_1:N:0:CAACACCT+AGCTACCA NW_026963362.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1431:12596:26872_1:N:0:CAACACCT+AGCTACCA NW_026963664.1 24122 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1433:30148:22768_1:N:0:CAACACCT+AGCTACCA NW_026963415.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1438:33458:12696_1:N:0:CAACACCT+AGCTACCA NW_026963415.1 1 Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1446:17273:20457_1:N:0:CAACACCT+AGCTACCA NW_026963619.1 23631 Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1454:39228:16325_1:N:0:CAACACCT+AGCTACCA NW_026963705.1 1 Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1458:20454:26662_1:N:0:CAACACCT+AGCTACCA NW_026963443.1 56341 Processed 38000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1472:50719:15120_1:N:0:CAACACCT+AGCTACCA NW_026963622.1 25207 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1473:3468:11716_1:N:0:CAACACCT+AGCTACCA NW_026963299.1 1 Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1498:41833:26074_1:N:0:CAACACCT+AGCTACCA NW_026963308.1 1 Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2137:36501:8662_1:N:0:CAACACCT+AGCTACCA NW_026963298.1 2989481 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2139:2732:1392_1:N:0:CAACACCT+AGCTACCA NW_026963308.1 1 Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2164:33417:5034_1:N:0:CAACACAT+AGCTACCA NW_026963443.1 56335 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2167:11107:9951_1:N:0:CAACACCT+AGCTACCA NW_026963553.1 40186 Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2189:25714:20583_1:N:0:CAACACCT+AGCTACCA NW_026963707.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2190:13033:26032_1:N:0:CAACACCT+AGCTACCA NW_026963611.1 2 Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2221:25892:20275_1:N:0:CAACACCT+AGCTACCA NW_026963309.1 2 Processed 53000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2230:35190:5945_1:N:0:CAACACCT+AGCTACCA NW_026963299.1 2 Processed 54000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2240:21797:6771_1:N:0:CAACACCT+AGCTACCA NW_026963377.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2240:21813:6771_1:N:0:CAACACCT+AGCTACCA NW_026963377.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2242:1566:15260_1:N:0:CAACACCT+AGCTACCA NW_026963307.1 124883 Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2257:13737:8228_1:N:0:CAACACCT+AGCTACCA NW_026963307.1 124878 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2260:51795:21746_1:N:0:CAACACCT+AGCTACCA NW_026963443.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2263:24791:27363_1:N:0:CAACACCT+AGCTACCA NW_026963437.1 23646 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2263:24791:27391_1:N:0:CAACACCT+AGCTACCA NW_026963437.1 23646 Processed 57000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2266:28190:3661_1:N:0:CAACACCT+AGCTACCA NW_026963772.1 22210 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2272:26272:15498_1:N:0:CAACACCT+AGCTACCA NW_026963812.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2272:26280:15512_1:N:0:CAACACCT+AGCTACCA NW_026963721.1 2 Processed 58000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2280:16359:6463_1:N:0:CAACACCT+AGCTACCA NW_026963680.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2280:16367:6477_1:N:0:CAACACCT+AGCTACCA NW_026963680.1 1 Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2296:34494:2779_1:N:0:CAACACCT+AGCTACCA NW_026963791.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2305:5467:24757_1:N:0:CAACACCT+AGCTACCA NW_026963803.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2305:5459:24771_1:N:0:CAACACCT+AGCTACCA NW_026963803.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2305:5475:24771_1:N:0:CAACACCT+AGCTACCA NW_026963803.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2305:5467:24785_1:N:0:CAACACCT+AGCTACCA NW_026963803.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2306:12669:6295_1:N:0:CAACACCT+AGCTACCA NW_026963415.1 1 Processed 61000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2316:6770:26536_1:N:0:CAACACCT+AGCTACCA NW_026963414.1 35638 Processed 62000000 sequence pairs so far Processed 63000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2328:10290:17473_1:N:0:CAACACCT+AGCTACCA NW_026963365.1 61328 Processed 64000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2346:26086:11002_1:N:0:CAACACCT+AGCTACCA NW_026963789.1 26203 Processed 65000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2348:19321:27531_1:N:0:CAACACCT+AGCTACCA NW_026963375.1 53641 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2348:19313:27545_1:N:0:CAACACCT+AGCTACCA NW_026963375.1 53641 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2352:49796:26466_1:N:0:CAACACCT+AGCTACCA NW_026963317.1 4467314 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2352:49820:26480_1:N:0:CAACACCT+AGCTACCA NW_026963317.1 4467314 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2358:46130:18552_1:N:0:CAACACCT+AGCTACCA NW_026963611.1 1 Processed 66000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2365:32616:15582_1:N:0:CAACACCT+AGCTACCA NW_026963299.1 1 Processed 67000000 sequence pairs so far Processed 68000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2390:15283:23454_1:N:0:CAACACCT+AGCTACCA NW_026963705.1 1 Processed 69000000 sequence pairs so far Processed 70000000 sequence pairs so far Processed 71000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2425:47652:20121_1:N:0:CAACACCT+AGCTACCA NW_026963688.1 1 Processed 72000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2431:44382:11996_1:N:0:CAACACCT+AGCTACCA NW_026963684.1 18465 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2431:48558:12276_1:N:0:CAAAACCT+AGCTACCA NW_026963378.1 1 Processed 73000000 sequence pairs so far Processed 74000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2449:32908:14826_1:N:0:CAACACCT+AGCTACCA NW_026963800.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2450:14765:14433_1:N:0:CAACACCT+AGCTACCA NW_026963725.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2450:7328:14868_1:N:0:CAACACCT+AGCTACCA NW_026963462.1 1 Processed 75000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2463:31896:28035_1:N:0:AAACACCT+AGCTACCA NW_026963378.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2463:31912:28035_1:N:0:CAACACCT+AGCTACCA NW_026963378.1 1 Processed 76000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2474:12264:28287_1:N:0:CAACACCT+AGCTACCA NW_026963443.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2477:12483:19000_1:N:0:CAACACCT+AGCTACCA NW_026963309.1 2 Processed 77000000 sequence pairs so far Processed 78000000 sequence pairs so far Processed 79000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1156:42011:21535_1:N:0:CAACACCT+AGCTACCA NW_026963348.1 1 Processed 80000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1215:19216:13033_1:N:0:CAACACCT+AGCTACCA NW_026963661.1 19676 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1231:46527:15064_1:N:0:CAACACCT+AGCTACCA NW_026963307.1 1 Processed 81000000 sequence pairs so far Processed 82000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1306:33393:8466_1:N:0:CAACACCT+AGCTACCA NW_026963291.1 1 Processed 83000000 sequence pairs so far Processed 84000000 sequence pairs so far Processed 85000000 sequence pairs so far Processed 86000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2183:22582:27237_1:N:0:CAACACCT+AGCTACCA NW_026963443.1 56335 Processed 87000000 sequence pairs so far Processed 88000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2330:2092:21493_1:N:0:CAACACAT+AGCTACCA NW_026963415.1 1 Processed 89000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2413:40118:29492_1:N:0:CAACACCT+AGCTACCA NW_026963305.1 1249887 Processed 90000000 sequence pairs so far Processed 91000000 sequence pairs so far 91280527 reads; of these: 91280527 (100.00%) were paired; of these: 36711987 (40.22%) aligned concordantly 0 times 16724060 (18.32%) aligned concordantly exactly 1 time 37844480 (41.46%) aligned concordantly >1 times 59.78% overall alignment rate 91280527 reads; of these: 91280527 (100.00%) were paired; of these: 36703406 (40.21%) aligned concordantly 0 times 16725316 (18.32%) aligned concordantly exactly 1 time 37851805 (41.47%) aligned concordantly >1 times 59.79% overall alignment rate Processed 91280527 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 365122108. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 365122108. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 365122108. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 365122108. Successfully deleted the temporary files 72M_R1.fastp-trim.fq.gz_C_to_T.fastq and 72M_R2.fastp-trim.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 91280527 Final Cytosine Methylation Report ================================= Total number of C's analysed: 2238195597 Total methylated C's in CpG context: 30036418 Total methylated C's in CHG context: 3202867 Total methylated C's in CHH context: 14705334 Total methylated C's in Unknown context: 352685 Total unmethylated C's in CpG context: 242033901 Total unmethylated C's in CHG context: 360839489 Total unmethylated C's in CHH context: 1587377588 Total unmethylated C's in Unknown context: 12348919 C methylated in CpG context: 11.0% C methylated in CHG context: 0.9% C methylated in CHH context: 0.9% C methylated in unknown context (CN or CHN): 2.8% Bismark completed in 0d 6h 17m 10s ==================== Bismark run complete ==================== Unable to flush stdout: Broken pipe