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/92M_R1.fastp-trim.fq.gz ../data/92M_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/92M_R1.fastp-trim.fq.gz and ../data/92M_R2.fastp-trim.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file 92M_R1.fastp-trim.fq.gz to 92M_R1.fastp-trim.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file 92M_R1.fastp-trim.fq.gz (92301777 sequences in total) Writing a G -> A converted version of the input file 92M_R2.fastp-trim.fq.gz to 92M_R2.fastp-trim.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file 92M_R2.fastp-trim.fq.gz (92301777 sequences in total) Input files are 92M_R1.fastp-trim.fq.gz_C_to_T.fastq and 92M_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 92M_R1.fastp-trim.fq.gz_C_to_T.fastq and 92M_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: LH00469:254:22HGFVLT4:2:1101:1218:1014_1:N:0:GTTGTTCG+CCAACTTC/1 99 NC_086377.1_CT_converted 72196896 2 131M = 72197004 239 GTTTTTTTTAATAATATTATATTTTTTAGTAAATTTTATTTTTTTTTTATAATGTATTTTGATATGATATTATATTGATTATATTTTTTAGATAGTTGTATAGAATATGTTTTTAAATTTGTTAATGGTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIII9III-IIIIIIIIIII99IIIIIIIIIIIIIIIIIIIIIII9I AS:i:-66 XS:i:-66 XN:i:0 XM:i:11 XO:i:0 XG:i:0 NM:i:11 MD:Z:0A13A2G29G5T10G22A0A5T13A2A19 YS:i:-60 YT:Z:CP LH00469:254:22HGFVLT4:2:1101:1218:1014_2:N:0:GTTGTTCG+CCAACTTC/2 147 NC_086377.1_CT_converted 72197004 2 131M = 72196896 -239 GTTTTTAAATTTGTTAATGGTTTTAATTAAGGTTTTTTTTTAATTTTATTGTAAATTTGATAATTTTTTTGATAATTGTAATAGATGAAATTTTAAATTGGTTATTTGATTAAGATAGATTTATAATATGT 9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIII AS:i:-60 XS:i:-56 XN:i:0 XM:i:10 XO:i:0 XG:i:0 NM:i:10 MD:Z:0A2A25T1A3A1A2A43T3T18T23 YS:i:-66 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 92M_R1.fastp-trim.fq.gz_C_to_T.fastq and 92M_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: LH00469:254:22HGFVLT4:2:1101:1218:1014_1:N:0:GTTGTTCG+CCAACTTC/1 83 NC_086377.1_GA_converted 71265141 6 131M = 71265032 -240 AAACCATTAACAAATTTAAAAACATATTCTATACAACTATCTAAAAAATATAATCAATATAATATCATATCAAAATACATTATAAAAAAAAAATAAAATTTACTAAAAAATATAATATTATTAAAAAAAAC I9IIIIIIIIIIIIIIIIIIIIIII99IIIIIIIIIII-III9IIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-36 XS:i:-36 XN:i:0 XM:i:6 XO:i:0 XG:i:0 NM:i:6 MD:Z:19T22T0T33T25A9T17 YS:i:-14 YT:Z:CP LH00469:254:22HGFVLT4:2:1101:1218:1014_2:N:0:GTTGTTCG+CCAACTTC/2 163 NC_086377.1_GA_converted 71265032 6 90M1D41M = 71265141 240 ACATATTATAAATCTATCTTAATCAAATAACCAATTTAAAATTTCATCTATTACAATTATCAAAAAAATTATCAAATTTACAATAAAATTAAAAAAAAACCTTAATTAAAACCATTAACAAATTTAAAAAC IIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9 AS:i:-14 XS:i:-18 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:90^A37T3 YS:i:-36 YT:Z:CP >>> Writing bisulfite mapping results to 92M_pe.bam <<< Reading in the sequence files ../data/92M_R1.fastp-trim.fq.gz and ../data/92M_R2.fastp-trim.fq.gz Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1113:43452:6295_1:N:0:GTTGTTCG+CCAACTTC NW_026963598.1 2 Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1129:8955:25640_1:N:0:GTTGTTCG+CCAACTTC NW_026963347.1 1227479 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1129:8971:25640_1:N:0:GTTGTTCG+CCAACTTC NW_026963347.1 1227479 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1143:41518:19616_1:N:0:GTTGTTCG+CCAACTTC NW_026963634.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1145:45888:19280_1:N:0:GTTGTTCG+CCAACTTC NW_026963678.1 1 Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1165:24160:28175_1:N:0:GTTGTTCG+CCAACTTC NW_026963397.1 22704 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1166:2716:3241_1:N:0:GTTGTTCG+CCAACTTC NW_026963776.1 1 Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1181:25770:23202_1:N:0:GTTGTTCG+CCAACTTC NW_026963598.1 2 Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1197:12879:1280_1:N:0:GTTGTTCG+CCAACTTC NW_026963598.1 3 Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1205:16189:13789_1:N:0:GTTGTTCG+CCAACTTC NW_026963456.1 1 Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1212:27154:26522_1:N:0:GTTGTTCG+CCAACTTC NW_026963645.1 1 Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far 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 LH00469:254:22HGFVLT4:2:1275:48914:10035_1:N:0:GTTGTTCG+CCAACTTC NW_026963680.1 23038 Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1282:17913:24141_1:N:0:GTTGTTCG+CCAACTTC NW_026963415.1 1 Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1296:33159:27979_1:N:0:GTTGTTCG+CCAACTTC NW_026963347.1 1227482 Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1324:31111:19112_1:N:0:GTTGTTCG+CCAACTTC NW_026963293.1 1 Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1344:29655:10175_1:N:0:GTTGTTCG+CCAACTTC NW_026963415.1 3 Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1353:9804:14756_1:N:0:GTTGTTCG+CCAACTTC NW_026963415.1 3 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1360:15606:18524_1:N:0:GTTGTTCG+CCAACTTC NW_026963740.1 1 Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1413:16302:12052_1:N:0:GTTGTTCG+CCAACTTC NW_026963598.1 2 Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1416:14053:11072_1:N:0:GTTGTTCG+CCAACTTC NW_026963456.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1424:3225:13873_1:N:0:GTTGTTCG+CCAACTTC NW_026963377.1 2 Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1426:34858:11926_1:N:0:GTTGTTCG+CCAACTTC NC_086385.1 63222867 Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1464:47903:4922_1:N:0:GTTGTTCG+CCAACTTC NW_026963307.1 124891 Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1492:23804:16100_1:N:0:GTTGTTCG+CCAATTTC NW_026963598.1 3 Processed 39000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2103:29922:9769_1:N:0:GTTGTTCG+CCAACTTC NW_026963391.1 25918 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2110:28853:17109_1:N:0:GTTGTTCG+CCAACTTC NW_026963751.1 1 Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2111:20405:13719_1:N:0:GTTGTTCG+CCAACTTC NW_026963415.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2115:16011:24855_1:N:0:GTTGTTCG+CCAACTTC NW_026963598.1 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 LH00469:254:22HGFVLT4:2:2149:41728:8718_1:N:0:GTTGTTCG+CCAACTTC NW_026963598.1 3 Processed 44000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2158:26054:26074_1:N:0:GTTGTTCG+CCAACTTC NW_026963415.1 2 Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2179:38540:27657_1:N:0:GTTGTTCG+CCAACTTC NW_026963598.1 1 Processed 47000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2183:45127:26312_1:N:0:GTTGTTCG+CCAACTTC NW_026963772.1 1 Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2214:28538:8298_1:N:0:GTTGTTCG+CCAACTTC NW_026963299.1 1 Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2241:14239:7948_1:N:0:GTTGTTCG+CCAACTTG NW_026963598.1 3 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2244:42562:17529_1:N:0:GTTGTTCG+CCAACTTC NW_026963404.1 1 Processed 53000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2249:41534:9643_1:N:0:GTTGTTCG+CCAACTTC NW_026963806.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2254:6519:29520_1:N:0:GTTGTTCG+CCAACTTC NW_026963657.1 17841 Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 57000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2292:23391:16535_1:N:0:GTTGTTCG+CCAACTTC NW_026963598.1 1 Processed 58000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2313:41550:20317_1:N:0:GTTGTTCG+CCAACTTC NW_026963415.1 1 Processed 59000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2322:23399:22068_1:N:0:GTTGTTCG+CCAACTTC NW_026963667.1 28285 Processed 60000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2333:8971:9223_1:N:0:GTTGTTCG+CCAACTTC NW_026963598.1 3 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2333:2538:29352_1:N:0:GTTGTTCG+CCAACTTC NW_026963598.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2334:7539:23637_1:N:0:GTTGTTCG+CCAACTTC NW_026963598.1 3 Processed 61000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2335:35295:29604_1:N:0:GTTGTTCG+CCAACTTC NW_026963456.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2335:35303:29618_1:N:0:GTTGTTCG+CCAACTTC NW_026963456.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2342:47247:20961_1:N:0:GTTGTTCG+CCAACTTC NW_026963598.1 1 Processed 62000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2347:20721:28245_1:N:0:GTTGTTCG+CCAACTTC NW_026963677.1 25110 Processed 63000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2358:23456:24575_1:N:0:GTTGTTCG+CCAACTTC NW_026963456.1 1 Processed 64000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2371:47393:21942_1:N:0:GTTGTTCG+CCAACTTC NW_026963598.1 1 Processed 65000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2382:23561:28623_1:N:0:GTTGTTCG+CCAACTTC NW_026963598.1 3 Processed 66000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2404:9392:29506_1:N:0:GTTGTTCG+CCAACTTC NW_026963415.1 1 Processed 67000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2416:15372:18482_1:N:0:GTTGTTCG+CCAACTTC NW_026963352.1 336915 Processed 68000000 sequence pairs so far 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 LH00469:254:22HGFVLT4:2:2455:20219:29702_1:N:0:GTTGTTCG+NCAACTTC NW_026963792.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2458:11900:23370_1:N:0:GTTGTTCG+CCAACTTC NW_026963598.1 3 Processed 72000000 sequence pairs so far Processed 73000000 sequence pairs so far Processed 74000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2485:46058:4390_1:N:0:GTTGTTCG+CCAACTTC NW_026963443.1 56337 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2493:21684:2429_1:N:0:GTTGTTCG+CCAACTTC NW_026963711.1 23006 Processed 75000000 sequence pairs so far Processed 76000000 sequence pairs so far 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 LH00586:122:22HTFTLT4:7:1268:27777:21549_1:N:0:GTTGTTCG+CCAACTTC NW_026963598.1 3 Processed 80000000 sequence pairs so far Processed 81000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1362:35303:22614_1:N:0:GTTGTTCG+CCAACTTC NW_026963415.1 3 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1397:4116:3732_1:N:0:GTTGTTCG+CCAACTTC NW_026963363.1 1 Processed 82000000 sequence pairs so far Processed 83000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1476:31508:26018_1:N:0:GTTGTTCG+CCAACTTC NW_026963598.1 3 Processed 84000000 sequence pairs so far Processed 85000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2165:30197:26410_1:N:0:GTTGTTCG+CCAACTTC NW_026963307.1 1 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2168:13324:25528_1:N:0:GTTGTTCG+CCAACTTC NW_026963598.1 2 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2188:48607:20373_1:N:0:GTTGTTCG+CCAACTTC NW_026963684.1 18469 Processed 86000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2224:5596:28035_1:N:0:GTTGTTCG+CCAACTTC NW_026963598.1 1 Processed 87000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2293:50840:19728_1:N:0:GTTGTTCG+CCAACTTC NW_026963307.1 2 Processed 88000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2302:50152:19238_1:N:0:GTTGTTCG+CCAACTTC NW_026963384.1 2 Processed 89000000 sequence pairs so far Processed 90000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2403:12693:19392_1:N:0:GTTGTTCG+CCAACTTC NW_026963415.1 3 Processed 91000000 sequence pairs so far Processed 92000000 sequence pairs so far 92301777 reads; of these: 92301777 (100.00%) were paired; of these: 38737211 (41.97%) aligned concordantly 0 times 18113093 (19.62%) aligned concordantly exactly 1 time 35451473 (38.41%) aligned concordantly >1 times 58.03% overall alignment rate 92301777 reads; of these: 92301777 (100.00%) were paired; of these: 38735370 (41.97%) aligned concordantly 0 times 18103454 (19.61%) aligned concordantly exactly 1 time 35462953 (38.42%) aligned concordantly >1 times 58.03% overall alignment rate Processed 92301777 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 369207108. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 369207108. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 369207108. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 369207108. Successfully deleted the temporary files 92M_R1.fastp-trim.fq.gz_C_to_T.fastq and 92M_R2.fastp-trim.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 92301777 Final Cytosine Methylation Report ================================= Total number of C's analysed: 2260814376 Total methylated C's in CpG context: 27892448 Total methylated C's in CHG context: 3406626 Total methylated C's in CHH context: 15981664 Total methylated C's in Unknown context: 389756 Total unmethylated C's in CpG context: 234815527 Total unmethylated C's in CHG context: 359049776 Total unmethylated C's in CHH context: 1619668335 Total unmethylated C's in Unknown context: 12759240 C methylated in CpG context: 10.6% C methylated in CHG context: 0.9% C methylated in CHH context: 1.0% C methylated in unknown context (CN or CHN): 3.0% Bismark completed in 0d 6h 24m 39s ==================== Bismark run complete ==================== Unable to flush stdout: Broken pipe