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/239M_R1.fastp-trim.fq.gz ../data/239M_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/239M_R1.fastp-trim.fq.gz and ../data/239M_R2.fastp-trim.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file 239M_R1.fastp-trim.fq.gz to 239M_R1.fastp-trim.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file 239M_R1.fastp-trim.fq.gz (107036137 sequences in total) Writing a G -> A converted version of the input file 239M_R2.fastp-trim.fq.gz to 239M_R2.fastp-trim.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file 239M_R2.fastp-trim.fq.gz (107036137 sequences in total) Input files are 239M_R1.fastp-trim.fq.gz_C_to_T.fastq and 239M_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 239M_R1.fastp-trim.fq.gz_C_to_T.fastq and 239M_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: LH00469:254:22HGFVLT4:2:1101:2206:1014_1:N:0:GAGCAGTA+TGAGCTGT/1 77 * 0 0 * * 0 0 GAATAAATGAATATTAAATATTATTGATTTATTATTATTAGTTTTTTATAAATTAATTTAATTATAAATTTATATATTGTTGATGATTTTAAATAGGAGGGAGGGTAGGAGGGGTTTTGATTTTGAAATTT IIIIIIIIIIIIIIIIIIIIIIIIII9IIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIII9IIIIIIIII9IIIIIIII9II9IIIIII9IIII-I-IIIII9I YT:Z:UP LH00469:254:22HGFVLT4:2:1101:2206:1014_2:N:0:GAGCAGTA+TGAGCTGT/2 141 * 0 0 * * 0 0 ATACTATATATCATTTTTTAAAATTTATTATTTTTATCACCTTAACAAAATAAAAAAACAAAACCTAAATATACTATTTAAAAAAAAATAAAACCTTAATCAAAACTCCAAAATCTAATATTTTTAATTTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-9IIIIIIIIIIIIIIIIIIIII-IIIIIIIIII9IIIIIIIIII-IIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 239M_R1.fastp-trim.fq.gz_C_to_T.fastq and 239M_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: LH00469:254:22HGFVLT4:2:1101:2206:1014_1:N:0:GAGCAGTA+TGAGCTGT/1 77 * 0 0 * * 0 0 GAATAAATGAATATTAAATATTATTGATTTATTATTATTAGTTTTTTATAAATTAATTTAATTATAAATTTATATATTGTTGATGATTTTAAATAGGAGGGAGGGTAGGAGGGGTTTTGATTTTGAAATTT IIIIIIIIIIIIIIIIIIIIIIIIII9IIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIII9IIIIIIIII9IIIIIIII9II9IIIIII9IIII-I-IIIII9I YT:Z:UP LH00469:254:22HGFVLT4:2:1101:2206:1014_2:N:0:GAGCAGTA+TGAGCTGT/2 141 * 0 0 * * 0 0 ATACTATATATCATTTTTTAAAATTTATTATTTTTATCACCTTAACAAAATAAAAAAACAAAACCTAAATATACTATTTAAAAAAAAATAAAACCTTAATCAAAACTCCAAAATCTAATATTTTTAATTTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-9IIIIIIIIIIIIIIIIIIIII-IIIIIIIIII9IIIIIIIIII-IIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIII YT:Z:UP >>> Writing bisulfite mapping results to 239M_pe.bam <<< Reading in the sequence files ../data/239M_R1.fastp-trim.fq.gz and ../data/239M_R2.fastp-trim.fq.gz Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1111:29420:9713_1:N:0:GAGCAGTA+TGAGCTGT NW_026963443.1 56348 Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1134:14692:26830_1:N:0:GAGCAGTA+TGAGCTGT NW_026963307.1 124908 Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1147:20559:26172_1:N:0:GAGCAGTA+TGAGCTGT NW_026963558.1 53359 Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1156:11674:8438_1:N:0:GAGCAGTA+TGAGCTGT NW_026963415.1 1 Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1206:30342:18118_1:N:0:GAGCAGTA+TGAGCTGT NW_026963443.1 1 Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1213:20098:7472_1:N:0:GAGCAGTA+TGAGCTGT NW_026963307.1 124881 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1214:19855:2737_1:N:0:GAGCAGTA+TGAGCTGT NW_026963415.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1214:33207:20975_1:N:0:GAGCAGTA+TGAGCTGT NW_026963377.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1214:33215:20989_1:N:0:GAGCAGTA+TGAGCTGT NW_026963377.1 2 Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1215:44374:16325_1:N:0:GAGCAGTA+TGAGCTGT NW_026963415.1 3 Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1228:43889:8312_1:N:0:GAGCAGTA+TGAGCTGT NW_026963717.1 1 Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1237:11010:24267_1:N:0:GAGCAGTA+TGAGCTGT NW_026963377.1 2 Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1245:20696:9685_1:N:0:GAGCAGTA+TGAGCTGT NW_026963415.1 1 Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1252:9934:4670_1:N:0:GAGCAGTA+TGAGCTGT NW_026963299.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1254:1696:26298_1:N:0:GAGCAGTA+TGAGCTGT NW_026963762.1 14841 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1256:8599:23595_1:N:0:GAGCAGTA+TGAGCTGT NW_026963352.1 336914 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1256:8591:23609_1:N:0:GAGCAGTA+TGAGCTGT NW_026963352.1 336914 Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1258:49408:24981_1:N:0:GAGCAGTA+TGAGCTGT NW_026963569.1 27454 Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1269:31759:6029_1:N:0:GAGCAGTA+TGAGCTGT NW_026963786.1 2 Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1277:45807:8018_1:N:0:GAGCAGTA+TGAGCTGT NW_026963443.1 56340 Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1284:31864:15176_1:N:0:GAGCAGTA+TGAGCTGT NC_086378.1 2 Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1302:17241:27125_1:N:0:GAGCAGTA+TGAGCTGT NW_026963415.1 3 Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1316:47830:22698_1:N:0:TAGCAGTA+TGAGCTGT NW_026963439.1 2 Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1336:3363:24869_1:N:0:GAGCAGTA+TGAGCTGT NW_026963307.1 124885 Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1345:46163:21325_1:N:0:GAGCAGTA+TGAGCTGT NW_026963335.1 2 Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1359:16747:17445_1:N:0:GAGCAGTA+TGAGCTGT NW_026963350.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1360:44844:25682_1:N:0:GAGCAGTA+TGAGCTGT NW_026963415.1 1 Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1383:30666:15036_1:N:0:AAGCAGTA+TGAGCTGT NW_026963415.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1383:23318:23496_1:N:0:GAGCAGTA+TGAGCTGT NW_026963363.1 2 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 Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1433:49545:20709_1:N:0:GAGCAGTA+TGAGCTGT NW_026963307.1 1 Processed 38000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1441:28789:22880_1:N:0:GAGCAGTA+TGAGCTGT NW_026963415.1 3 Processed 39000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1450:3630:13397_1:N:0:GAGCAGTA+TGAGCTGT NW_026963786.1 17988 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1450:15153:19784_1:N:0:GAGCAGTA+TGAGCTGT NW_026963443.1 56335 Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1459:38418:20807_1:N:0:GAGCAGTA+TGAGCTGT NW_026963380.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1459:38410:20821_1:N:0:GAGCAGTA+TGAGCTGT NW_026963380.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1459:38427:20821_1:N:0:GAGCAGTA+TGAGCTGT NW_026963380.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1459:38418:20835_1:N:0:GAGCAGTA+TGAGCTGT NW_026963380.1 2 Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1475:47830:27573_1:N:0:GAGCAGTA+TGAGCTGT NW_026963598.1 3 Processed 43000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1492:31087:24505_1:N:0:GAGCCGTA+TGAGCTGT NW_026963732.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1493:44512:24043_1:N:0:GAGCAGTA+TGAGCTGT NW_026963795.1 1 Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2112:37439:12108_1:N:0:GAGCAGTA+TGAGCTGT NW_026963415.1 1 Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2152:16197:4502_1:N:0:GAGCAGTA+TGAGCTGT NW_026963684.1 18480 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2152:16205:4516_1:N:0:GAGCAGTA+TGAGCTGT NW_026963684.1 18480 Processed 50000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2155:36387:9531_1:N:0:GAGCAGTA+TGAGCTGT NW_026963742.1 18832 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2157:51916:12318_1:N:0:GAGCAGTA+TGCGCTGT NW_026963415.1 1 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 LH00469:254:22HGFVLT4:2:2184:49796:13047_1:N:0:GAGCAGTA+TGAGCTGT NW_026963468.1 1 Processed 54000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2195:13066:21942_1:N:0:GAGCAGTA+TGAGCTGT NW_026963378.1 3 Processed 55000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2202:37035:22110_1:N:0:GAGCAGTA+TGAGCTGT NW_026963415.1 3 Processed 56000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2218:28684:15526_1:N:0:GAGCAGTA+TGAGCTGT NW_026963303.1 2 Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2264:37585:9643_1:N:0:GAGCAGTA+TGAGCTGT NW_026963742.1 18832 Processed 62000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2271:30852:11492_1:N:0:GAGCAGTA+TGAGCTGT NW_026963743.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2275:25762:7135_1:N:0:GAGCAGTA+TGAGCTGT NW_026963415.1 1 Processed 63000000 sequence pairs so far Processed 64000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2288:6139:12612_1:N:0:GAGCAGTA+TGAGCTGT NW_026963743.1 1 Processed 65000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2302:5426:11044_1:N:0:GAGCAGTA+TGAGCTGT NW_026963443.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2308:40045:17795_1:N:0:GAGCAGTA+TGAGCTGT NW_026963742.1 18831 Processed 66000000 sequence pairs so far Processed 67000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2319:4585:17907_1:N:0:GAGCAGTA+TGAGCTGT NW_026963684.1 18470 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2321:42529:29268_1:N:0:GAGCAGTA+TGAGCTGT NW_026963484.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2322:19110:2625_1:N:0:GAGCAGTA+TGAGCTGT NW_026963415.1 3 Processed 68000000 sequence pairs so far Processed 69000000 sequence pairs so far Processed 70000000 sequence pairs so far Processed 71000000 sequence pairs so far Processed 72000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2373:23148:12584_1:N:0:GAGCAGTA+TGAGCTGT NW_026963415.1 3 Processed 73000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2380:47223:22908_1:N:0:GAGCAGTA+TGAGCTGT NC_086380.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2380:23812:27153_1:N:0:GAGCAGTA+TGAGCTGT NW_026963443.1 56341 Processed 74000000 sequence pairs so far Processed 75000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2404:37180:9587_1:N:0:GAGCAGTA+TGAGCTGT NW_026963687.1 26549 Processed 76000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2419:14101:14826_1:N:0:GAGCAGTA+TGAGCTGT NW_026963743.1 1 Processed 77000000 sequence pairs so far Processed 78000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2432:36420:5889_1:N:0:GAGCAGTA+TGAGCTGT NW_026963748.1 22377 Processed 79000000 sequence pairs so far Processed 80000000 sequence pairs so far Processed 81000000 sequence pairs so far Processed 82000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2477:29946:10259_1:N:0:GAGCAGTA+TGAGCTGT NW_026963308.1 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 Processed 87000000 sequence pairs so far Processed 88000000 sequence pairs so far Processed 89000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1245:33571:19700_1:N:0:GAGCAGTA+TGAGCTGT NW_026963308.1 1 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1267:45799:9068_1:N:0:GAGCAGTA+TGAGCTGT NW_026963684.1 18523 Processed 90000000 sequence pairs so far Processed 91000000 sequence pairs so far Processed 92000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1375:32042:1700_1:N:0:GAGCAGTA+TGAGCTGT NW_026963415.1 1 Processed 93000000 sequence pairs so far Processed 94000000 sequence pairs so far Processed 95000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1461:19418:5875_1:N:0:GAGCAGTA+TGAGCTGT NW_026963352.1 336907 Processed 96000000 sequence pairs so far Processed 97000000 sequence pairs so far Processed 98000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2166:39713:25318_1:N:0:GAGCAGTA+TGAGCTGT NW_026963519.1 2 Processed 99000000 sequence pairs so far Processed 100000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2244:42651:16563_1:N:0:GAGCAGTA+TGAGCTGT NW_026963531.1 22258 Processed 101000000 sequence pairs so far Processed 102000000 sequence pairs so far Processed 103000000 sequence pairs so far Processed 104000000 sequence pairs so far Processed 105000000 sequence pairs so far Processed 106000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2473:2359:12066_1:N:0:GAGCAGTA+TGAGCTGT NW_026963684.1 18469 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2479:2942:13159_1:N:0:GAGCAGTA+TGAGCTGT NW_026963443.1 56334 Processed 107000000 sequence pairs so far 107036137 reads; of these: 107036137 (100.00%) were paired; of these: 45812914 (42.80%) aligned concordantly 0 times 20991206 (19.61%) aligned concordantly exactly 1 time 40232017 (37.59%) aligned concordantly >1 times 57.20% overall alignment rate 107036137 reads; of these: 107036137 (100.00%) were paired; of these: 45820928 (42.81%) aligned concordantly 0 times 20995365 (19.62%) aligned concordantly exactly 1 time 40219844 (37.58%) aligned concordantly >1 times 57.19% overall alignment rate Processed 107036137 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 428144548. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 428144548. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 428144548. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 428144548. Successfully deleted the temporary files 239M_R1.fastp-trim.fq.gz_C_to_T.fastq and 239M_R2.fastp-trim.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 107036137 Final Cytosine Methylation Report ================================= Total number of C's analysed: 2571308564 Total methylated C's in CpG context: 35552729 Total methylated C's in CHG context: 4173216 Total methylated C's in CHH context: 19714079 Total methylated C's in Unknown context: 524336 Total unmethylated C's in CpG context: 259600078 Total unmethylated C's in CHG context: 406065309 Total unmethylated C's in CHH context: 1846203153 Total unmethylated C's in Unknown context: 14480727 C methylated in CpG context: 12.0% C methylated in CHG context: 1.0% C methylated in CHH context: 1.1% C methylated in unknown context (CN or CHN): 3.5% Bismark completed in 0d 7h 20m 42s ==================== Bismark run complete ==================== Unable to flush stdout: Broken pipe