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/71M_R1.fastp-trim.fq.gz ../data/71M_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/71M_R1.fastp-trim.fq.gz and ../data/71M_R2.fastp-trim.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file 71M_R1.fastp-trim.fq.gz to 71M_R1.fastp-trim.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file 71M_R1.fastp-trim.fq.gz (89919803 sequences in total) Writing a G -> A converted version of the input file 71M_R2.fastp-trim.fq.gz to 71M_R2.fastp-trim.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file 71M_R2.fastp-trim.fq.gz (89919803 sequences in total) Input files are 71M_R1.fastp-trim.fq.gz_C_to_T.fastq and 71M_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 71M_R1.fastp-trim.fq.gz_C_to_T.fastq and 71M_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: LH00469:254:22HGFVLT4:2:1101:1121:1014_1:N:0:NTGCCTGT+NGATTGCG/1 77 * 0 0 * * 0 0 TTGATTTGTGAGTTTGATTGTTTTTTTAATATTTGATGTTTTTTTTTTTGAATATGAAATTAGTGATTGTTGTTGAATGTTTTTGATTTAGTTATTTTTTTATAATATAAAAATAATATGTTTAGTTTTTT IIIII-IIII9II-IIIIIIIIIIIIII-IIIIIIIIIIIIIIIIII9IIIIIIIIIII-IIIIIIIIII9III-IIIIIIIIIIIIIIIIIIII--IIIIII9IIII-II9III9-II9IIIIIIII-II YT:Z:UP LH00469:254:22HGFVLT4:2:1101:1121:1014_2:N:0:NTGCCTGT+NGATTGCG/2 141 * 0 0 * * 0 0 ATTTTAAAAATATAAATTTTTAATTTAACAACTTTTTCACATCTATAACATACATTTACAAAAAAAAAAAATTTAAAATTTATTTTTATTTAATATCCTTTTATTCTAAATAAACTAAACATATTATTTTT IIIIIIIIIIII9IIIIIIII9IIIIIIIIIIIIIII9IIII9IIII9II99IIIIIIIIIIIII9II9IIIIIIIIIIIIIIIIIIII99IIII9IIIIIIIIIII9IIIIIIIIIII9IIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 71M_R1.fastp-trim.fq.gz_C_to_T.fastq and 71M_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: LH00469:254:22HGFVLT4:2:1101:1121:1014_1:N:0:NTGCCTGT+NGATTGCG/1 77 * 0 0 * * 0 0 TTGATTTGTGAGTTTGATTGTTTTTTTAATATTTGATGTTTTTTTTTTTGAATATGAAATTAGTGATTGTTGTTGAATGTTTTTGATTTAGTTATTTTTTTATAATATAAAAATAATATGTTTAGTTTTTT IIIII-IIII9II-IIIIIIIIIIIIII-IIIIIIIIIIIIIIIIII9IIIIIIIIIII-IIIIIIIIII9III-IIIIIIIIIIIIIIIIIIII--IIIIII9IIII-II9III9-II9IIIIIIII-II YT:Z:UP LH00469:254:22HGFVLT4:2:1101:1121:1014_2:N:0:NTGCCTGT+NGATTGCG/2 141 * 0 0 * * 0 0 ATTTTAAAAATATAAATTTTTAATTTAACAACTTTTTCACATCTATAACATACATTTACAAAAAAAAAAAATTTAAAATTTATTTTTATTTAATATCCTTTTATTCTAAATAAACTAAACATATTATTTTT IIIIIIIIIIII9IIIIIIII9IIIIIIIIIIIIIII9IIII9IIII9II99IIIIIIIIIIIII9II9IIIIIIIIIIIIIIIIIIII99IIII9IIIIIIIIIII9IIIIIIIIIII9IIIIIIIIIII YT:Z:UP >>> Writing bisulfite mapping results to 71M_pe.bam <<< Reading in the sequence files ../data/71M_R1.fastp-trim.fq.gz and ../data/71M_R2.fastp-trim.fq.gz Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1101:4326:16170_1:N:0:ATGCCTGT+AGATTGCG NW_026963578.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1109:44763:24085_1:N:0:ATGCCTGT+AGATTGCG NW_026963608.1 22018 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1109:44981:25556_1:N:0:ATGCCTGT+AGATTGCG NW_026963668.1 19432 Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1154:24128:20023_1:N:0:ATGCCTGT+AGATTGCG NW_026963608.1 22014 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1156:47789:1896_1:N:0:ATGCCTGT+AGATTGCG NW_026963468.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1160:22922:2527_1:N:0:ATGCCTGT+AGATTGCG NW_026963291.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1163:24095:6435_1:N:0:ATGCCTGT+AGATTGCG NW_026963725.1 2 Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1173:34178:23104_1:N:0:ATGCCTGT+AGATTGCG NW_026963725.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1173:10419:23216_1:N:0:ATGCCTGT+AGATTGCG NC_086376.1 3 Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1180:23391:26368_1:N:0:ATGCCTGT+AGATTGCG NW_026963660.1 1 Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1189:35950:12332_1:N:0:ATGCCTGT+AGATTGCG NW_026963517.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1192:16553:3129_1:N:0:ATGCCTGT+AGATTGCG NW_026963395.1 45140 Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1205:16618:15680_1:N:0:ATGCCTGT+AGATTGCG NW_026963795.1 2 Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1216:51188:13411_1:N:0:ATGCCTGT+AGATTGCG NW_026963774.1 18497 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1216:51196:13425_1:N:0:ATGCCTGT+AGATTGCG NW_026963774.1 18497 Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1222:41162:9167_1:N:0:ATGCCTGT+AGATTGCG NW_026963771.1 24029 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1226:46300:28623_1:N:0:ATGCCTGT+AGATTGCG NW_026963725.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1227:18309:22782_1:N:0:ATGCCTGT+AGACTGCG NW_026963725.1 1 Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1236:13583:24379_1:N:0:ATGCCTGT+AGATTGCG NW_026963719.1 2 Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1244:10476:21213_1:N:0:ATGCCTGT+AGATTGCG NW_026963800.1 1 Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1249:33935:28651_1:N:0:ATGCCTGT+AGATTGCG NW_026963797.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1250:17233:22880_1:N:0:ATGCCTGT+AGATTGCG NW_026963711.1 3 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1252:46656:17165_1:N:0:ATGCCTGT+AGATTGCG NW_026963308.1 1 Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1260:43687:1939_1:N:0:ATGCCTAT+AGATTGCG NW_026963305.1 1249879 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1260:25131:27671_1:N:0:ATGCCTGT+AGATTGCG NW_026963405.1 20649 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1266:38831:23006_1:N:0:ATGCCTGT+AGATTGCG NW_026963725.1 2 Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1273:50630:12472_1:N:0:ATGCCTGT+AGATTGCG NW_026963636.1 18737 Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1284:25948:15330_1:N:0:ATGCCTGT+AGATTGCG NW_026963743.1 21265 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1289:6527:16927_1:N:0:ATGCCTGT+AGATTGCG NW_026963598.1 29333 Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1312:16165:28623_1:N:0:ATGCCTGT+AGATTGCG NW_026963578.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1312:16157:28637_1:N:0:ATGCCTGT+AGATTGCG NW_026963578.1 2 Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1325:14757:20247_1:N:0:ATGCCTGT+AGATTGCG NW_026963415.1 1 Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1329:11334:21045_1:N:0:ATGCCTGT+AGATTGCG NW_026963442.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1332:27389:26536_1:N:0:ATGCCTGT+AGATTGCG NC_086384.1 60197980 Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1339:49416:4768_1:N:0:ATGCCTGT+AGATTGCG NW_026963415.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1340:42853:23777_1:N:0:ATGCCTGT+AGATTGCG NW_026963771.1 24028 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1344:12944:24057_1:N:0:ATGCCTGT+AGATTGCG NW_026963786.1 1 Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1353:5993:5496_1:N:0:ATGCCTGT+AGATTGCG NW_026963377.1 2 Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1373:17662:18608_1:N:0:ATGCCTGT+AGATTGCG NW_026963315.1 4066330 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1373:17654:18622_1:N:0:ATGCCTGT+AGATTGCG NW_026963315.1 4066330 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1373:17662:18636_1:N:0:ATGCCTGT+AGATTGCG NW_026963315.1 4066330 Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1387:27049:22138_1:N:0:ATGCCTGT+AGATTGCG NW_026963753.1 2 Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1393:31694:20653_1:N:0:ATGCCTGT+AGATTGCG NW_026963634.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1394:12305:15386_1:N:0:ATGCCTGT+AGATTGCG NW_026963514.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1403:46972:12472_1:N:0:ATGCCTGT+AGATTGCG NW_026963743.1 1 Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1443:21765:7948_1:N:0:ATGCCTGT+AGATTGCG NW_026963608.1 22014 Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1456:26126:3479_1:N:0:ATGCCTGT+AGATTGCG NW_026963299.1 1 Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1460:43063:8116_1:N:0:ATGCCTGT+AGATTGCG NW_026963303.1 1 Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1470:47716:12444_1:N:0:ATGCCTGT+AGATTGCG NW_026963771.1 24028 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1470:47733:12444_1:N:0:ATGCCTGT+AGATTGCG NW_026963771.1 24028 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1476:5621:12500_1:N:0:ATGCCTGT+AGATTGCG NW_026963502.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1476:5613:12514_1:N:0:ATGCCTGT+AGATTGCG NW_026963502.1 1 Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1485:25091:15330_1:N:0:ATGCCTGT+AGATTGCG NW_026963636.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1488:43339:7275_1:N:0:ATGCCTGT+AGATTGCG NW_026963608.1 22014 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1489:1558:25976_1:N:0:ATGCCTGT+AGATTGCG NW_026963395.1 45150 Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1497:31920:18244_1:N:0:ATGCCTGT+AGATTGCG NC_007687.1 18545 Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2113:2222:14602_1:N:0:ATGCCTGT+AGATTGCG NW_026963405.1 20646 Processed 38000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2118:34032:5987_1:N:0:ATGCCTGT+AGATTGCG NW_026963548.1 28470 Processed 39000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2128:30003:5426_1:N:0:ATGCCTGT+AGATTGCG NW_026963415.1 2 Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2140:38920:5426_1:N:0:ATGCCTGT+AGATTGCG NW_026963725.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2141:32325:9811_1:N:0:ATGCCTGT+AGATTGCG NW_026963608.1 22022 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2146:37650:14546_1:N:0:ATGCCTGT+AGATTGCG NW_026963593.1 2 Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2161:29970:18930_1:N:0:ATGCCTGT+AGATTGCG NW_026963548.1 28471 Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far 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 LH00469:254:22HGFVLT4:2:2220:49723:28946_1:N:0:ATGCCTGT+AGATTGCG NW_026963785.1 13079 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2223:10282:23903_1:N:0:ATGCCTGT+AGATTGCG NW_026963319.1 249871 Processed 48000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2233:9513:14279_1:N:0:ATGCCTGT+AGATTGCG NW_026963608.1 22014 Processed 49000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2243:26458:12010_1:N:0:ATGCCTGT+AGATTGCG NW_026963405.1 20649 Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2291:31095:18216_1:N:0:ATGCCTGT+AGATTGCG NW_026963538.1 33132 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2296:29849:1378_1:N:0:ATGCCTGT+AGATTGCG NW_026963585.1 2 Processed 54000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2304:2416:26564_1:N:0:ATGCCTGT+AGATTGCG NW_026963608.1 22022 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2313:38014:6911_1:N:0:ATGCCTGT+AGATTGCG NW_026963581.1 2 Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2327:28870:21788_1:N:0:ATGCCTGT+AGATTGCG NW_026963533.1 25114 Processed 57000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2341:41647:20149_1:N:0:ATGCCTGT+AGATTGCG NW_026963711.1 23015 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2343:25341:6687_1:N:0:ATGCCTGT+AGATTGCG NW_026963711.1 22996 Processed 58000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2348:13705:9153_1:N:0:ATGCCTGT+AGATTGCG NW_026963319.1 249870 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2348:13713:9167_1:N:0:ATGCCTGT+AGATTGCG NW_026963319.1 249870 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2358:1890:17137_1:N:0:ATGCCTGT+AGATTGCG NW_026963502.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2358:1906:17137_1:N:0:ATGCCTGT+AGATTGCG NW_026963502.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2359:14441:5973_1:N:0:ATGCCTGT+AGATTGCG NW_026963474.1 24588 Processed 59000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2364:20672:14237_1:N:0:ATGCCTGT+AGATTGCG NW_026963299.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2365:46964:29352_1:N:0:ATGCCTGT+AGATTGCG NW_026963608.1 22016 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2367:50120:25402_1:N:0:ATGCCTGT+AGATTGCG NW_026963511.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2367:50136:25402_1:N:0:ATGCCTGT+AGATTGCG NW_026963511.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2367:50144:25416_1:N:0:ATGCCTGT+AGATTGCG NW_026963511.1 1 Processed 60000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2380:33474:19925_1:N:0:ATGCCTGT+AGATTGCG NW_026963529.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2380:33482:19939_1:N:0:ATGCCTGT+AGATTGCG NW_026963529.1 1 Processed 61000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2386:33118:26396_1:N:0:ATGCCTGT+AGATTGCG NW_026963554.1 2 Processed 62000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2410:25722:11968_1:N:0:ATGCCTGT+AGATTGCG NW_026963585.1 2 Processed 63000000 sequence pairs so far Processed 64000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2434:13009:20723_1:N:0:ATGCCTGT+AGATTGCG NW_026963719.1 3 Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2450:38694:16717_1:N:0:ATGCCTGT+AGATTGCG NW_026963308.1 1 Processed 67000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2464:7854:22054_1:N:0:ATGCCTGT+AGATTGCG NW_026963773.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2470:34178:4950_1:N:0:ATGCCTGG+AGATTGCG NW_026963335.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2470:34154:4964_1:N:0:ATGCCTGG+AGATTGCG NW_026963335.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2470:34170:4964_1:N:0:ATGCCTGG+AGATTGCG NW_026963335.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2470:34186:4964_1:N:0:ATGCCTGC+AGATTGCG NW_026963335.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2470:47061:12094_1:N:0:ATGCCTGT+AGATTGCG NW_026963684.1 18481 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2470:4569:19308_1:N:0:ATGCCTGT+AGATTGCG NW_026963347.1 1227497 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2470:32835:20919_1:N:0:ATGCCTGT+AGATTGCG NW_026963738.1 23715 Processed 68000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2477:31022:7752_1:N:0:ATGCCTGT+AGATTGCG NW_026963766.1 21441 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2481:23464:17893_1:N:0:ATGCCTGT+AGATTGCG NW_026963333.1 249907 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2481:23480:17921_1:N:0:ATGCCTGT+AGATTGCG NW_026963333.1 249907 Processed 69000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2483:15348:6365_1:N:0:ATGCCTGT+AGATTGCG NW_026963415.1 2 Processed 70000000 sequence pairs so far Processed 71000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1136:34534:17809_1:N:0:ATGCCTGT+AGATTGCG NW_026963585.1 2 Processed 72000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1168:12685:6071_1:N:0:ATGCCTGT+AGATTGCG NW_026963711.1 1 Processed 73000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1223:9513:7023_1:N:0:ATGCCTGT+AGATTGCG NW_026963299.1 1 Processed 74000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1263:10848:7065_1:N:0:ATGCCTGT+AGATTGCG NW_026963718.1 1 Processed 75000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1292:51892:8550_1:N:0:ATGCCTGT+AGATTGCG NW_026963725.1 1 Processed 76000000 sequence pairs so far Processed 77000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1370:43290:14644_1:N:0:ATGCCTGT+AGATTGCG NW_026963684.1 18491 Processed 78000000 sequence pairs so far Processed 79000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1453:16691:28301_1:N:0:ATGCCTGT+AGATTGCG NW_026963377.1 2 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1453:16707:28301_1:N:0:ATGCCTGT+AGATTGCG NW_026963377.1 2 Processed 80000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2118:14401:16717_1:N:0:ATGCCTGT+AGATTGCG NW_026963455.1 21333 Processed 81000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2163:1623:14854_1:N:0:ATGCCTGT+AGATTGCG NW_026963704.1 3 Processed 82000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2172:9270:8480_1:N:0:ATGCCTGT+AGATTGCG NW_026963326.1 2 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2187:4302:28904_1:N:0:ATGCCTGT+AGATTGCG NW_026963711.1 2 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2195:27826:23342_1:N:0:ATGCCTGT+AGATTGCG NW_026963542.1 23780 Processed 83000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2219:13179:23202_1:N:0:ATGCCTGT+AGATTGCG NW_026963335.1 1 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2226:3533:19308_1:N:0:ATGCCTGT+AGATTGCG NW_026963608.1 22027 Processed 84000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2258:28967:5258_1:N:0:ATGCCTGT+AGATTGCG NW_026963749.1 2 Processed 85000000 sequence pairs so far Processed 86000000 sequence pairs so far Processed 87000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2383:4156:25962_1:N:0:ATGCCTGT+AGATTGCG NW_026963372.1 501115 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2417:43330:19280_1:N:0:ATGCCTGT+AGATTGCG NW_026963333.1 249909 Processed 88000000 sequence pairs so far Processed 89000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2483:47012:15120_1:N:0:ATGCCTGT+AGATTGCG NW_026963608.1 22012 89919803 reads; of these: 89919803 (100.00%) were paired; of these: 35297181 (39.25%) aligned concordantly 0 times 16043682 (17.84%) aligned concordantly exactly 1 time 38578940 (42.90%) aligned concordantly >1 times 60.75% overall alignment rate 89919803 reads; of these: 89919803 (100.00%) were paired; of these: 35313264 (39.27%) aligned concordantly 0 times 16042748 (17.84%) aligned concordantly exactly 1 time 38563791 (42.89%) aligned concordantly >1 times 60.73% overall alignment rate Processed 89919803 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 359679212. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 359679212. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 359679212. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 359679212. Successfully deleted the temporary files 71M_R1.fastp-trim.fq.gz_C_to_T.fastq and 71M_R2.fastp-trim.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 89919803 Final Cytosine Methylation Report ================================= Total number of C's analysed: 2221550433 Total methylated C's in CpG context: 31067155 Total methylated C's in CHG context: 3232739 Total methylated C's in CHH context: 14582016 Total methylated C's in Unknown context: 356650 Total unmethylated C's in CpG context: 246967520 Total unmethylated C's in CHG context: 360577382 Total unmethylated C's in CHH context: 1565123621 Total unmethylated C's in Unknown context: 12250721 C methylated in CpG context: 11.2% 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 11m 29s ==================== Bismark run complete ==================== Unable to flush stdout: Broken pipe