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/107M_R1.fastp-trim.fq.gz ../data/107M_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/107M_R1.fastp-trim.fq.gz and ../data/107M_R2.fastp-trim.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file 107M_R1.fastp-trim.fq.gz to 107M_R1.fastp-trim.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file 107M_R1.fastp-trim.fq.gz (93644807 sequences in total) Writing a G -> A converted version of the input file 107M_R2.fastp-trim.fq.gz to 107M_R2.fastp-trim.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file 107M_R2.fastp-trim.fq.gz (93644807 sequences in total) Input files are 107M_R1.fastp-trim.fq.gz_C_to_T.fastq and 107M_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 107M_R1.fastp-trim.fq.gz_C_to_T.fastq and 107M_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: LH00469:254:22HGFVLT4:2:1101:1898:1014_1:N:0:GATCGAGT+GACGAACT/1 99 NW_026963295.1_CT_converted 968607 0 92M2D39M = 968583 -157 TTAATTATTTATTTTGTTATTTTGATATATTTATATTGTTATTTTGATATTTAAATTGTTATATTGATATATTTATTTTGTTATTTTGATATTTAAATTGTAATATTGATATATTTATTTTGTTATTTTGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII9IIIIIIIII9IIIIIIIIIIIIIIIIII AS:i:-53 XS:i:-53 XN:i:0 XM:i:7 XO:i:1 XG:i:2 NM:i:9 MD:Z:0A28A62^AA2T0T5T2T25T0 YS:i:-59 YT:Z:CP LH00469:254:22HGFVLT4:2:1101:1898:1014_2:N:0:GATCGAGT+GACGAACT/2 147 NW_026963295.1_CT_converted 968583 0 25M4D106M = 968607 157 TGATATATTTATATTGTTATTTTGATATTTAAATTGTTATATTGATATATTTATTTTGTTATTTTGATATTTAAATTGTAATATTGATATATTTATTTTGTTATTTTGATATAATTATATTGTTATTTTGA 9IIIIIIIIIIIIIII9IIIII9II9II9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIII AS:i:-59 XS:i:-59 XN:i:0 XM:i:7 XO:i:1 XG:i:4 NM:i:11 MD:Z:25^TAAT6T0T7T8A4A24T36T14 YS:i:-53 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 107M_R1.fastp-trim.fq.gz_C_to_T.fastq and 107M_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: LH00469:254:22HGFVLT4:2:1101:1898:1014_1:N:0:GATCGAGT+GACGAACT/1 83 NC_086376.1_GA_converted 15392383 2 59M2I20M2D44M1I5M = 15392445 197 TCAAAATAACAAAATAAATATATCAATATTACAATTTAAATATCAAAATAACAAAATAAATATATCAATATAACAATTTAAATATCAAAATAACAATATAAATATATCAAAATAACAAAATAAATAATTAA IIIIIIIIIIIIIIIIII9IIIIIIIII9IIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-96 XS:i:-84 XN:i:0 XM:i:11 XO:i:3 XG:i:5 NM:i:16 MD:Z:29A5A7T10T11A8A3^TT15A13T7T0T7C2 YS:i:-47 YT:Z:CP LH00469:254:22HGFVLT4:2:1101:1898:1014_2:N:0:GATCGAGT+GACGAACT/2 163 NC_086376.1_GA_converted 15392445 2 104M4D27M = 15392383 -197 TCAAAATAACAATATAATTATATCAAAATAACAAAATAAATATATCAATATTACAATTTAAATATCAAAATAACAAAATAAATATATCAATATAACAATTTAAATATCAAAATAACAATATAAATATATCA IIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II9II9IIIII9IIIIIIIIIIIIIII9 AS:i:-47 XS:i:-59 XN:i:0 XM:i:5 XO:i:1 XG:i:4 NM:i:9 MD:Z:51A29T8A7A0A4^TAAT27 YS:i:-96 YT:Z:CP >>> Writing bisulfite mapping results to 107M_pe.bam <<< Reading in the sequence files ../data/107M_R1.fastp-trim.fq.gz and ../data/107M_R2.fastp-trim.fq.gz Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1114:12831:10189_1:N:0:GATCGAGT+GACGAACT NW_026963415.1 2 Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1171:36533:12696_1:N:0:GATCGAGT+GACGAACT NW_026963743.1 1 Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1184:20648:13943_1:N:0:GATCGAGT+GACGAACT NW_026963684.1 18469 Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1208:45370:11800_1:N:0:GATCGAGT+GACGAACT NW_026963743.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1208:45378:11814_1:N:0:GATCGAGT+GACGAACT NW_026963743.1 1 Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1214:37156:26914_1:N:0:GATCGAGT+GACGAACT NW_026963372.1 501135 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1214:37148:26928_1:N:0:GATCGAGT+GACGAACT NW_026963372.1 501135 Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1224:47862:7289_1:N:0:GATCGAGT+GACGAACT NW_026963578.1 1 Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far 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 LH00469:254:22HGFVLT4:2:1284:31192:21185_1:N:0:GATCGAGT+GACGAACT NW_026963707.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1289:44868:14041_1:N:0:GATCGAGT+GACGAACT NW_026963307.1 124902 Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1319:33150:2863_1:N:0:GATCGAGT+GACGAACT NW_026963585.1 49266 Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1325:19167:26116_1:N:0:GATCGAGT+GACGAACT NW_026963743.1 1 Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1360:8671:5174_1:N:0:GATCGAGT+GACGAACT NW_026963743.1 1 Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1369:35182:11506_1:N:0:GATCGAGT+GACGAACT NW_026963628.1 24170 Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1377:7077:16226_1:N:0:GATCGAGT+GACGAACT NW_026963585.1 2 Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1386:21781:22348_1:N:0:GATCGAGT+GACGAACT NW_026963319.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1388:19426:7794_1:N:0:GATCGAGT+GACGAACT NC_086380.1 80675443 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1388:19434:7808_1:N:0:GATCGAGT+GACGAACT NC_086380.1 80675443 Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1432:48615:10385_1:N:0:GATCGAGT+GACGAACT NW_026963415.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1439:24799:10035_1:N:0:GATAGAGT+GACGAACT NW_026963743.1 1 Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1443:12297:12486_1:N:0:GATCGAGT+GACGAACT NW_026963684.1 18481 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1445:4876:28693_1:N:0:GATCGAGT+GACGAACT NW_026963326.1 1 Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1464:3776:11884_1:N:0:GATCGAGT+GACGAACT NW_026963760.1 1 Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1468:13316:12542_1:N:0:GATCGAGT+GACGAACT NW_026963319.1 1 Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2104:19054:14041_1:N:0:GATCGAGT+GACGAACT NW_026963300.1 356515 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2104:19046:14055_1:N:0:GATCGAGT+GACGAACT NW_026963300.1 356515 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2104:19062:14055_1:N:0:GATCGAGT+GACGAACT NW_026963300.1 356515 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2104:19054:14069_1:N:0:GATCGAGT+GACGAACT NW_026963300.1 356515 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2104:19046:14083_1:N:0:GATCGAGT+GACGAACT NW_026963300.1 356515 Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2121:49262:17389_1:N:0:GATCGAGT+GACGAACT NW_026963340.1 4220836 Processed 46000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2130:27769:15848_1:N:0:GATCGAGT+GACGAACT NW_026963448.1 1 Processed 47000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2141:9286:4586_1:N:0:GATCGAGT+GACGAACT NW_026963724.1 1 Processed 48000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2151:39810:18790_1:N:0:GATCGAGT+GACGAACT NW_026963415.1 2 Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2165:37010:15652_1:N:0:GATCGAGT+GACGAACT NW_026963290.1 2 Processed 51000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2175:38386:6827_1:N:0:GATCGAGT+GACGAACT NW_026963443.1 56354 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2177:27186:2737_1:N:0:GATCGAGT+GACGAACT NW_026963684.1 18502 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2178:39770:19308_1:N:0:GATCGAGT+GACGAACT NW_026963812.1 1 Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2203:2732:26522_1:N:0:GATCGAGT+GACGAACT NW_026963415.1 1 Processed 54000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2210:43403:28399_1:N:0:GATCGAGT+GACGAACT NW_026963352.1 336910 Processed 55000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2223:48420:15092_1:N:0:GATCGAGT+GACGAACT NW_026963684.1 18509 Processed 56000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2247:17492:28231_1:N:0:GATCGAGT+GACGAACT NW_026963309.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2248:49424:3886_1:N:0:GATCGAGT+GACGAACT NW_026963443.1 56339 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2248:49416:3900_1:N:0:GATCGAGT+GACGAACT NW_026963443.1 56339 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2248:49432:3900_1:N:0:GATCGAGT+GACGAACT NW_026963443.1 56339 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2248:49424:3914_1:N:0:GATCGAGT+GACGAACT NW_026963443.1 56339 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2250:19677:1728_1:N:0:GATCGAGT+GACGAACT NW_026963352.1 336899 Processed 59000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2258:38313:24491_1:N:0:GATCGAGT+GACGAACT NW_026963372.1 501132 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2258:38329:24491_1:N:0:GATCGAGT+GACGAACT NW_026963372.1 501132 Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2274:28878:12865_1:N:0:GATCGAGT+GACGAACT NW_026963743.1 1 Processed 62000000 sequence pairs so far Processed 63000000 sequence pairs so far Processed 64000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2307:42934:13971_1:N:0:GATCGAGT+GACGAACT NW_026963443.1 56334 Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2333:21910:24813_1:N:0:GATCGAGT+GACGAACT NW_026963415.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2334:7409:7752_1:N:0:GATCGAGT+GACGAACT NW_026963509.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2334:7425:7752_1:N:0:GATCGAGT+GACGAACT NW_026963509.1 2 Processed 67000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2340:45030:28497_1:N:0:GATCGAGT+GACGAACT NW_026963684.1 18465 Processed 68000000 sequence pairs so far Processed 69000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2357:41186:20303_1:N:0:GATNGAGT+GACGAACT NW_026963303.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2358:12232:18482_1:N:0:GATCGAGT+GACGAACT NW_026963351.1 17520 Processed 70000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2368:21158:1770_1:N:0:GATCGAGT+GACGAACT NW_026963743.1 1 Processed 71000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2376:29711:2037_1:N:0:GATCGAGT+GACGAACT NW_026963372.1 501125 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2379:33442:5833_1:N:0:GATCGAGT+GACGAACT NW_026963415.1 2 Processed 72000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2383:41704:15148_1:N:0:GATCGAGT+GACGAACT NW_026963684.1 18489 Processed 73000000 sequence pairs so far Processed 74000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2409:4666:14153_1:N:0:GATCGAGT+GACGAACT NW_026963415.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2409:42780:24183_1:N:0:GATCGAGT+GACGAACT NW_026963377.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2409:42813:24183_1:N:0:GATCGAGT+GACGAACT NW_026963377.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2409:42788:24197_1:N:0:GATCGAGT+GACGAACT NW_026963377.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2409:42804:24197_1:N:0:GATCGAGT+GACGAACT NW_026963377.1 2 Processed 75000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2426:5208:4838_1:N:0:GATCGAGT+GACGAACT NW_026963315.1 4066329 Processed 76000000 sequence pairs so far Processed 77000000 sequence pairs so far Processed 78000000 sequence pairs so far Processed 79000000 sequence pairs so far Processed 80000000 sequence pairs so far Processed 81000000 sequence pairs so far Processed 82000000 sequence pairs so far Processed 83000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2497:17233:29492_1:N:0:GATCGAGT+GACGAACT NW_026963377.1 2 Processed 84000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1176:35117:27307_1:N:0:GATCGAGT+GACGAACT NW_026963322.1 898871 Processed 85000000 sequence pairs so far Processed 86000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1362:25641:15470_1:N:0:GATCGAGT+GACGAACT NW_026963377.1 2 Processed 87000000 sequence pairs so far Processed 88000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2128:23796:29590_1:N:0:GATCGAGT+GACGAACT NW_026963642.1 22065 Processed 89000000 sequence pairs so far Processed 90000000 sequence pairs so far Processed 91000000 sequence pairs so far Processed 92000000 sequence pairs so far Processed 93000000 sequence pairs so far 93644807 reads; of these: 93644807 (100.00%) were paired; of these: 40998878 (43.78%) aligned concordantly 0 times 18527110 (19.78%) aligned concordantly exactly 1 time 34118819 (36.43%) aligned concordantly >1 times 56.22% overall alignment rate 93644807 reads; of these: 93644807 (100.00%) were paired; of these: 40995132 (43.78%) aligned concordantly 0 times 18528338 (19.79%) aligned concordantly exactly 1 time 34121337 (36.44%) aligned concordantly >1 times 56.22% overall alignment rate Processed 93644807 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 374579228. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 374579228. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 374579228. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 374579228. Successfully deleted the temporary files 107M_R1.fastp-trim.fq.gz_C_to_T.fastq and 107M_R2.fastp-trim.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 93644807 Final Cytosine Methylation Report ================================= Total number of C's analysed: 2259292627 Total methylated C's in CpG context: 31029789 Total methylated C's in CHG context: 3432382 Total methylated C's in CHH context: 16112864 Total methylated C's in Unknown context: 403573 Total unmethylated C's in CpG context: 227529716 Total unmethylated C's in CHG context: 357498950 Total unmethylated C's in CHH context: 1623688926 Total unmethylated C's in Unknown context: 12561884 C methylated in CpG context: 12.0% C methylated in CHG context: 1.0% C methylated in CHH context: 1.0% C methylated in unknown context (CN or CHN): 3.1% Bismark completed in 0d 11h 28m 44s ==================== Bismark run complete ==================== Unable to flush stdout: Broken pipe