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 /home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/data/ (absolute path is '/home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/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/8TB_HDD_03/sr320/github/timeseries_molecular/D-Apul/code'): /home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/10--1E7_R1_001.fastp-trim.fq.gz /home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/10--1E7_R2_001.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/8TB_HDD_03/sr320/github/timeseries_molecular/D-Apul/output/14-Apul-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/8TB_HDD_03/sr320/github/timeseries_molecular/D-Apul/code Now reading in and storing sequence information of the genome specified in: /home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/data/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/10--1E7_R1_001.fastp-trim.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/10--1E7_R2_001.fastp-trim.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file 10--1E7_R1_001.fastp-trim.fq.gz to 10--1E7_R1_001.fastp-trim.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file 10--1E7_R1_001.fastp-trim.fq.gz (39254990 sequences in total) Writing a G -> A converted version of the input file 10--1E7_R2_001.fastp-trim.fq.gz to 10--1E7_R2_001.fastp-trim.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file 10--1E7_R2_001.fastp-trim.fq.gz (39254990 sequences in total) Input files are 10--1E7_R1_001.fastp-trim.fq.gz_C_to_T.fastq and 10--1E7_R2_001.fastp-trim.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/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 10--1E7_R1_001.fastp-trim.fq.gz_C_to_T.fastq and 10--1E7_R2_001.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: LH00526:197:22KFKVLT4:3:1101:39624:1070_1:N:0:GCCTTAAC+AGCTCCTA/1 99 ptg000008l_CT_converted 21054450 42 125M = 21054648 323 GATAATAGGTTATATTTGATATATATTGGTAATAATAGAGTAAAAGATATATTTTTTATTTTTTGGGTTTTGTATATTTTAGGTTTAGTTTAGTTTTTATTTAAGTAAGTATGTAATGAAGGAAT IIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII9I9IIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIII99IIII9III9IIIII-II-IIII-II AS:i:-18 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:108T4G7A3 YS:i:-6 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:39624:1070_2:N:0:GCCTTAAC+AGCTCCTA/2 147 ptg000008l_CT_converted 21054648 42 125M = 21054450 -323 TGGAATAGAGGATATTGATTTTTTAGTGGTTAAGTTTATAGAAGTTGAGGATAAGAATTTTGTATTTTTGAATTATGTTAATGAATTTAATAATGAAATTGAGTTGTTGTAAGAATAAATAAATG IIIIIIIIIIII9I9IIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII9IIIIIIIIIII9IIIIIII-IIIIIIIIIIIIIIIII9IIIIIIIIII9IIIII9II-IIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:69T55 YS:i:-18 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 10--1E7_R1_001.fastp-trim.fq.gz_C_to_T.fastq and 10--1E7_R2_001.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: LH00526:197:22KFKVLT4:3:1101:39624:1070_1:N:0:GCCTTAAC+AGCTCCTA/1 77 * 0 0 * * 0 0 GATAATAGGTTATATTTGATATATATTGGTAATAATAGAGTAAAAGATATATTTTTTATTTTTTGGGTTTTGTATATTTTAGGTTTAGTTTAGTTTTTATTTAAGTAAGTATGTAATGAAGGAAT IIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII9I9IIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIII99IIII9III9IIIII-II-IIII-II YT:Z:UP LH00526:197:22KFKVLT4:3:1101:39624:1070_2:N:0:GCCTTAAC+AGCTCCTA/2 141 * 0 0 * * 0 0 CATTTATTTATTCTTACAACAACTCAATTTCATTATTAAATTCATTAACATAATTCAAAAATACAAAATTCTTATCCTCAACTTCTATAAACTTAACCACTAAAAAATCAATATCCTCTATTCCA IIIIIIIIIIIIIIIII-II9IIIII9IIIIIIIIII9IIIIIIIIIIIIIIIII-IIIIIII9IIIIIIIIIII9IIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIII9I9IIIIIIIIIIII YT:Z:UP >>> Writing bisulfite mapping results to 10--1E7_pe.bam <<< Reading in the sequence files /home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/10--1E7_R1_001.fastp-trim.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/10--1E7_R2_001.fastp-trim.fq.gz Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1104:32398:21171_1:N:0:GCCTTAAC+AGCTCCTA ptg000130l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1123:6608:27265_1:N:0:GCCTTAAC+AGCTCCTA ptg000160l 1 Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1145:38103:3760_1:N:0:GCCTTAAC+AGCTCCTA ptg000012l 20102977 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1190:36501:8830_1:N:0:GCCTTAAC+AGCTCCTA ptg000118l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1190:36517:8830_1:N:0:GCCTTAAC+AGCTCCTA ptg000118l 1 Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1230:13948:8396_1:N:0:GCCTTAAC+AGCTCCTA ptg000108l 1 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1244:34704:22978_1:N:0:GCCTTAAC+AGCTCCTA ptg000016l 13007867 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 LH00526:197:22KFKVLT4:3:1350:28870:9853_1:N:0:GCCTTAAC+AGCTCCTA ptg000066l 66345 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1377:47069:4180_1:N:0:GCCTTAAC+AGCTCCTA ptg000083l 2 Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1382:13753:1840_1:N:0:GCCTTAAC+AGCTCCTA ptg000113l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1411:20381:25247_1:N:0:GCCTTAAC+AGCTCCTA ptg000096l 1 Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1439:34283:16423_1:N:0:GCCTTAAC+AGCTCCTA ptg000056l 59112 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1444:33531:23468_1:N:0:GCCTTAAC+AGCTCCTA ptg000146l 38991 Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1486:35319:9727_1:N:0:GCCTTAAC+AGCTCCTA ntLink_0 1 Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2115:11034:5791_1:N:0:GCCTTAAC+AGCTCCTA ptg000127l 1 Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2144:23213:23623_1:N:0:GCCTTAAC+AGCTCCTA ptg000095l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2144:23229:23623_1:N:0:GCCTTAAC+AGCTCCTA ptg000095l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2144:6470:23917_1:N:0:GCCTTAAC+AGCTCCTA ptg000024l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2160:25965:27321_1:N:0:GCCTTAAC+AGCTCCTA ptg000113l 59560 Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2251:4925:11548_1:N:0:GCCTTAAC+AGCTCCTA ptg000066l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2264:10533:4194_1:N:0:GCCTTAAC+AGCTCCTA ptg000096l 1 Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2283:41785:29100_1:N:0:GCCTTAAC+AGCTCCTA ptg000132l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2304:26159:9279_1:N:0:GCCTTAAC+AGCTCCTA ptg000024l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2304:47433:27223_1:N:0:GCCTTAAC+AGCTCCTA ntLink_4 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2304:47449:27223_1:N:0:GCCTTAAC+AGCTCCTA ntLink_4 1 Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2330:50411:2709_1:N:0:GCCTTAAC+AGCTCCTA ptg000066l 66351 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2332:19539:26648_1:N:0:GCCTTAAC+AGCTCCTA ptg000155l 36784 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2364:2416:24883_1:N:0:GCCTTAAC+AGCTCCTA ptg000029c 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2370:30011:13901_1:N:0:GCCTTAAC+AGCTCCTA ptg000159l 2 Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2384:32503:4656_1:N:0:GCCTTAAC+AGCTCCTA ptg000101l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2402:42537:18916_1:N:0:GCCTTAAC+AGCTCCTA ptg000046l 39588 Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2438:47927:22222_1:N:0:GCCTTAAC+AGCTCCTA ptg000018l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2463:18811:3507_1:N:0:GCCTTAAC+AGCTCCTA ptg000048l 1 Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2483:19944:3479_1:N:0:GCCTTAAC+AGCTCCTA ptg000021l 1 Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1111:25082:25990_1:N:0:GCCTTAAC+AGCTCCTA ptg000155l 36785 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1131:38386:6155_1:N:0:GCCTTAAC+AGCTCCTA ptg000130l 35791 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1134:42133:20513_1:N:0:GCCTTAAC+AGCTCCTA ptg000092l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1138:38232:10287_1:N:0:GCCTTAAC+AGCTCCTA ptg000096l 2 Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1155:13138:16100_1:N:0:GCCTTAAC+AGCTCCTA ptg000106l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1165:40191:12921_1:N:0:GCCTTAAC+AGCTCCTA ptg000020l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1165:40183:12935_1:N:0:GCCTTAAC+AGCTCCTA ptg000020l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1173:8833:13131_1:N:0:GCCTTAAC+AGCTCCTA ntLink_7 1 Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1205:28862:4292_1:N:0:GCCTTAAC+AGCTCCTA ptg000056l 59115 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1214:6721:4432_1:N:0:GCCTTAAC+AGCTCCTA ptg000114l 51156 Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1236:6600:17165_1:N:0:GCCTTAAC+AGCTCCTA ptg000055l 50538 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1237:39033:15680_1:N:0:GCCTTAAC+AGCTCCTA ntLink_7 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1237:39050:15680_1:N:0:GCCTTAAC+AGCTCCTA ntLink_7 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1242:20980:15918_1:N:0:GCCTTAAC+AGCTCCTA ntLink_0 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1242:20988:15932_1:N:0:GCCTTAAC+AGCTCCTA ntLink_0 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1242:20996:15946_1:N:0:GCCTTAAC+AGCTCCTA ntLink_0 1 Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1276:40417:24071_1:N:0:GCCTTAAC+AGCTCCTA ptg000112l 1 Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1305:38775:18986_1:N:0:GCCTTAAC+AGCTCCTA ptg000117l 30005 Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1343:6244:28791_1:N:0:GCCTTAAC+AGCTCCTA ptg000097l 1 Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1367:47886:26942_1:N:0:GCCTTAAC+AGCTCCTA ptg000124l 54849 Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1413:49027:17655_1:N:0:GCCTTAAC+AGCTCCTA ptg000159l 21853 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1420:50524:27111_1:N:0:GCCTTAAC+AGCTCCTA ptg000126l 1 Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1448:32001:7346_1:N:0:GCCTTAAC+AGCTCCTA ptg000057l 39948 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1450:9918:24141_1:N:0:GCCTTAAC+AGCTCCTA ptg000115l 42041 Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1471:32374:25388_1:N:0:GCCTTAAC+AGCTCCTA ptg000030l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1474:41146:28749_1:N:0:GCCTTAAC+AGCTCCTA ptg000012l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1477:3954:22754_1:N:0:GCCTTAAC+AGCTCCTA ptg000108l 75358 Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2118:27413:15932_1:N:0:GCCTTAAC+AGCTCCTA ptg000093l 36765 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2121:10047:2205_1:N:0:GCCTTAAC+AGCTCCTA ptg000133l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2126:9699:12921_1:N:0:GCCTTAAC+AGCTCCTA ptg000118l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2130:40911:24645_1:N:0:GCCTTAAC+AGCTCCTA ptg000039l 1139419 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2134:41728:3760_1:N:0:GCCTTAAC+AGCTCCTA ptg000066l 66343 Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2151:17136:24673_1:N:0:GCCTTAAC+AGCTCCTA ptg000094l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2172:14692:25598_1:N:0:GCCTTAAC+AGCTCCTA ptg000054l 36051 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2176:45677:4600_1:N:0:GCCTTAAC+AGCTCCTA ptg000060c 88492 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2180:39754:9951_1:N:0:GCCTTAAC+AGCTCCTA ptg000089l 46433 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2190:27462:3914_1:N:0:GCCTTAAC+AGCTCCTA ptg000160l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2190:27470:3928_1:N:0:GCCTTAAC+AGCTCCTA ptg000160l 2 Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2194:27065:14742_1:N:0:GCCTTAAC+AGCTCCTA ptg000129l 33365 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2217:8987:16675_1:N:0:GCCTTAAC+AGCTCCTA ptg000176l 41272 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2219:9974:19336_1:N:0:GCCTTAAC+AGCTCCTA ptg000047l 1 Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2254:15364:13369_1:N:0:GCCTTAAC+AGCTCCTA ptg000094l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2258:50897:13159_1:N:0:GCCTTAAC+AGCTCCTA ptg000009l 19095996 Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2297:21320:27685_1:N:0:GCCTTAAC+AGCTCCTA ptg000083l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2298:9918:1476_1:N:0:GCCTTAAC+AGCTCCTA ptg000109l 39600 Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2386:44585:15848_1:N:0:GCCTTAAC+AGCTCCTA ptg000185l 34514 Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far 39254990 reads; of these: 39254990 (100.00%) were paired; of these: 15398684 (39.23%) aligned concordantly 0 times 7964289 (20.29%) aligned concordantly exactly 1 time 15892017 (40.48%) aligned concordantly >1 times 60.77% overall alignment rate 39254990 reads; of these: 39254990 (100.00%) were paired; of these: 15413381 (39.26%) aligned concordantly 0 times 7963443 (20.29%) aligned concordantly exactly 1 time 15878166 (40.45%) aligned concordantly >1 times 60.74% overall alignment rate Processed 39254990 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 157019960. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 157019960. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 157019960. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 157019960. Successfully deleted the temporary files 10--1E7_R1_001.fastp-trim.fq.gz_C_to_T.fastq and 10--1E7_R2_001.fastp-trim.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 39254990 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1152438422 Total methylated C's in CpG context: 21959954 Total methylated C's in CHG context: 1220418 Total methylated C's in CHH context: 4968994 Total methylated C's in Unknown context: 63587 Total unmethylated C's in CpG context: 155140616 Total unmethylated C's in CHG context: 192792022 Total unmethylated C's in CHH context: 776356418 Total unmethylated C's in Unknown context: 2925906 C methylated in CpG context: 12.4% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in unknown context (CN or CHN): 2.1% Bismark completed in 0d 2h 39m 46s ==================== Bismark run complete ====================