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/2A3_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/2A3_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/2A3_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/2A3_R2_001.fastp-trim.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file 2A3_R1_001.fastp-trim.fq.gz to 2A3_R1_001.fastp-trim.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file 2A3_R1_001.fastp-trim.fq.gz (33813626 sequences in total) Writing a G -> A converted version of the input file 2A3_R2_001.fastp-trim.fq.gz to 2A3_R2_001.fastp-trim.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file 2A3_R2_001.fastp-trim.fq.gz (33813626 sequences in total) Input files are 2A3_R1_001.fastp-trim.fq.gz_C_to_T.fastq and 2A3_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 2A3_R1_001.fastp-trim.fq.gz_C_to_T.fastq and 2A3_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: LH00652:104:22KG7JLT4:7:1101:12828:1084_1:N:0:TCTACGCA+GGCTATTG/1 77 * 0 0 * * 0 0 TTTTTTAATTAATGAGAATTAAAATTAAAATTAATTGTATTATGTATGTGTGATTTTTTTTGTGTTTTGAGTGAGTTATATGTAATTGTTAGGTGATTGGTTTATTGTGTTGTTTGTTTTTGTTG II9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIII-IIIII9-II YT:Z:UP LH00652:104:22KG7JLT4:7:1101:12828:1084_2:N:0:TCTACGCA+GGCTATTG/2 141 * 0 0 * * 0 0 ACTTACTTCTACTTATCCATTACTTAAAAACTACTAAACAAATAATCACACAACTTCAAATTACAACACAATTACTCCCACCAATCACAACAAAAACAAACAACACAATAAACCAATCACCTAAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 2A3_R1_001.fastp-trim.fq.gz_C_to_T.fastq and 2A3_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: LH00652:104:22KG7JLT4:7:1101:12828:1084_1:N:0:TCTACGCA+GGCTATTG/1 83 ptg000008l_GA_converted 5399774 6 32M5D93M = 5399687 -217 CAACAAAAACAAACAACACAATAAACCAATCACCTAACAATTACATATAACTCACTCAAAACACAAAAAAAATCACACATACATAATACAATTAATTTTAATTTTAATTCTCATTAATTAAAAAA II-9IIIII-IIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II AS:i:-20 XS:i:-26 XN:i:0 XM:i:0 XO:i:1 XG:i:5 NM:i:5 MD:Z:32^CAATT93 YS:i:-20 YT:Z:CP LH00652:104:22KG7JLT4:7:1101:12828:1084_2:N:0:TCTACGCA+GGCTATTG/2 163 ptg000008l_GA_converted 5399687 6 119M5D6M = 5399774 217 ACTTACTTCTACTTATCCATTACTTAAAAACTACTAAACAAATAATCACACAACTTCAAATTACAACACAATTACTCCCACCAATCACAACAAAAACAAACAACACAATAAACCAATCACCTAAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-20 XS:i:-32 XN:i:0 XM:i:0 XO:i:1 XG:i:5 NM:i:5 MD:Z:119^CAATT6 YS:i:-20 YT:Z:CP >>> Writing bisulfite mapping results to 2A3_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/2A3_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/2A3_R2_001.fastp-trim.fq.gz Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1116:23442:14031_1:N:0:TCTACGCA+GGCTATTG ptg000115l 1 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1116:23458:14031_1:N:0:TCTACGCA+GGCTATTG ptg000115l 1 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1139:10514:23700_1:N:0:TCTACGCA+GGCTATTG ptg000160l 1 Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1151:28433:21388_1:N:0:TCTACGCA+GGCTATTG ptg000066l 66348 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1158:30496:27119_1:N:0:TCTACGCA+GGCTATTG ptg000093l 1 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1162:26411:11635_1:N:0:TCTACGCA+GGCTATTG ptg000024l 2 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1195:47420:26054_1:N:0:TCTACGCA+GGCTATTG ptg000004l 1 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1195:47429:26068_1:N:0:TCTACGCA+GGCTATTG ptg000004l 1 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1231:17544:18501_1:N:0:TCTACGCA+GGCTATTG ptg000093l 36762 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1231:17560:18501_1:N:0:TCTACGCA+GGCTATTG ptg000093l 36762 Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1241:20901:1532_1:N:0:TCTACGCA+GGCTATTG ptg000057l 39968 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1242:8597:1575_1:N:0:TCTACGCA+GGCTATTG ptg000066l 66340 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1257:19162:1294_1:N:0:TCTACGCA+GGCTATTG ptg000113l 1 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1261:26912:4657_1:N:0:TCTACGCA+GGCTATTG ptg000025l 21443080 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1280:15238:14816_1:N:0:TCTACGCA+GGCTATTG ptg000011l 1 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1280:15246:14830_1:N:0:TCTACGCA+GGCTATTG ptg000011l 1 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1285:47704:2752_1:N:0:TCTACGCA+GGCTATTG ptg000075l 1 Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1374:20796:12084_1:N:0:TCTACGCA+GGCTATTG ptg000090l 49494 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1374:20804:12098_1:N:0:TCTACGCA+GGCTATTG ptg000090l 49494 Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1403:7415:5134_1:N:0:TCTACGCA+GGCTATTG ptg000006l 1 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1416:10368:16974_1:N:0:TCTACGCA+GGCTATTG ptg000024l 3 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1417:5765:9253_1:N:0:TCTACGCA+GGCTATTG ptg000066l 66356 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1417:10506:22985_1:N:0:TCTACGCA+GGCTATTG ptg000046l 2 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1419:23717:6857_1:N:0:TCTACGCA+GGCTATTG ptg000101l 1 Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1457:48666:8735_1:N:0:TCTACGCA+GGCTATTG ptg000092l 1 Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:1495:32203:14858_1:N:0:TCTACGCA+GGCTATTG ptg000046l 2 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2104:32519:14424_1:N:0:TCTACGCA+GGCTATTG ptg000124l 54857 Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2119:47420:18039_1:N:0:TCTACGCA+GGCTATTG ptg000125l 1 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2149:15376:19034_1:N:0:TCTACGCA+GGCTATTG ptg000024l 3 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2154:42453:15405_1:N:0:TCTACGCA+GGCTATTG ptg000096l 1 Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2182:43885:10879_1:N:0:TCTACGCA+GGCTATTG ptg000089l 1 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2198:21209:11313_1:N:0:TCTACGCA+GGCTATTG ptg000093l 1 Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2230:31977:28198_1:N:0:TCTACGCA+GGCTATTG ptg000108l 75349 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2230:31985:28212_1:N:0:TCTACGCA+GGCTATTG ptg000108l 75349 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2244:32203:9001_1:N:0:TCTACGCA+GGCTATTG ptg000075l 1 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2244:13273:16540_1:N:0:TCTACGCA+GGCTATTG ptg000106l 40356 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2244:13264:16554_1:N:0:TCTACGCA+GGCTATTG ptg000106l 40356 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2259:27689:25844_1:N:0:TCTACGCA+GGCTATTG ptg000011l 1 Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2263:7642:19454_1:N:0:TCTACGCA+GGCTATTG ptg000090l 2 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2274:21977:3620_1:N:0:TCTACGCA+GGCTATTG ptg000048l 1 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2279:15756:13583_1:N:0:TCTACGCA+GGCTATTG ptg000057l 39942 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2294:7181:16273_1:N:0:TCTACGCA+GGCTATTG ptg000089l 1 Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2359:33117:27035_1:N:0:TCTACGCA+GGCTATTG ptg000092l 28988 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2366:41620:26600_1:N:0:TCTACGCA+GGCTATTG ptg000066l 66414 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2368:28466:11888_1:N:0:TCTACGCA+GGCTATTG ptg000052l 52608 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2377:33465:14802_1:N:0:TCTACGCA+GGCTATTG ptg000006l 1 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2406:17568:15180_1:N:0:TCTACGCA+GGCTATTG ptg000006l 3 Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2444:38424:10472_1:N:0:TCTACGCA+GGCTATTG ptg000160l 32599 Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2477:10692:1701_1:N:0:TCTACGCA+GGCTATTG ptg000123l 44479 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:7:2494:11121:10094_1:N:0:TCTACGCA+GGCTATTG ptg000129l 1 Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:1157:4147:10318_1:N:0:TCTACGCA+GGCTATTG ptg000116l 1 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:1190:16622:8300_1:N:0:TCTACGCA+GGCTATTG ptg000088l 1 Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:1198:42170:8048_1:N:0:TCTACGCA+GGCTATTG ptg000082l 1 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:1198:42178:8062_1:N:0:TCTACGCA+GGCTATTG ptg000082l 1 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:1214:29760:16091_1:N:0:TCTACGCA+GGCTATTG ptg000133l 2 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:1223:35827:27693_1:N:0:TCTACGCA+GGCTATTG ptg000098l 55098 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:1236:16800:6199_1:N:0:TCTACGCA+GGCTATTG ptg000096l 1 Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:1262:32794:25606_1:N:0:TCTACGCA+GGCTATTG ptg000073l 1 Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:1345:21063:2709_1:N:0:TCTACGCA+GGCTATTG ptg000129l 1 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:1345:21079:2709_1:N:0:TCTACGCA+GGCTATTG ptg000129l 1 Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:1407:4163:9898_1:N:0:TCTACGCA+GGCTATTG ptg000046l 39575 Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:1431:26030:29025_1:N:0:TCTACGCA+GGCTATTG ptg000088l 2 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:1434:13022:29109_1:N:0:TCTACGCA+GGCTATTG ptg000106l 1 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:1434:13038:29109_1:N:0:TCTACGCA+GGCTATTG ptg000106l 1 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:1471:52080:8903_1:N:0:TCTACGCA+GGCTATTG ptg000066l 2 Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:1476:35277:14158_1:N:0:TCTACGCA+GGCTATTG ptg000004l 2 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:1487:45220:29613_1:N:0:TCTACGCA+GGCTATTG ptg000115l 1 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2116:26686:7460_1:N:0:TCTACGCA+GGCTATTG ptg000077l 42492 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2117:43934:28450_1:N:0:TCTACGCA+GGCTATTG ptg000046l 39578 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2117:43958:28492_1:N:0:TCTACGCA+GGCTATTG ptg000046l 39578 Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2127:27932:14914_1:N:0:TCTACGCA+GGCTATTG ptg000088l 1 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2131:13442:15853_1:N:0:TCTACGCA+GGCTATTG ptg000024l 1 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2135:28093:2836_1:N:0:TCTACGCA+GGCTATTG ptg000066l 2 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2140:15902:26362_1:N:0:TCTACGCA+GGCTATTG ptg000025l 21443081 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2145:9317:12154_1:N:0:TCTACGCA+GGCTATTG ptg000092l 2 Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2192:24057:4363_1:N:0:TCTACGCA+GGCTATTG ptg000006l 3 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2201:21621:28898_1:N:0:TCTACGCA+GGCTATTG ptg000098l 1 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2216:20109:22635_1:N:0:TCTACGCA+GGCTATTG ptg000181l 31369 Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2234:39605:3718_1:N:0:TCTACGCA+GGCTATTG ptg000075l 54138 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2243:11493:14101_1:N:0:TCTACGCA+GGCTATTG ptg000027l 2 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2254:49945:23308_1:N:0:TCTACGCA+GGCTATTG ptg000015l 14997091 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2266:3176:11187_1:N:0:TCTACGCA+GGCTATTG ptg000011l 1 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2266:3192:11187_1:N:0:TCTACGCA+GGCTATTG ptg000011l 1 Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2303:47768:6815_1:N:0:TCTACGCA+GGCTATTG ntLink_0 96482 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2314:43909:28884_1:N:0:TCTACGCA+GGCTATTG ptg000057l 39964 Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2317:4171:15685_1:N:0:TCTACGCA+GGCTATTG ptg000093l 1 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2317:4163:15699_1:N:0:TCTACGCA+GGCTATTG ptg000093l 1 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2318:31459:20855_1:N:0:TCTACGCA+GGCTATTG ptg000092l 1 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2336:21694:24821_1:N:0:TCTACGCA+GGCTATTG ptg000048l 1 Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2386:10999:10304_1:N:0:TCTACGCA+GGCTATTG ptg000088l 1 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2389:14462:20561_1:N:0:TCTACGCA+GGCTATTG ptg000053l 71566 Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2457:33959:1560_1:N:0:TCTACGCA+GGCTATTG ptg000128l 2 Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2464:28765:15685_1:N:0:TCTACGCA+GGCTATTG ptg000146l 38993 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2466:27017:7193_1:N:0:TCTACGCA+GGCTATTG ptg000066l 66352 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2476:15869:14536_1:N:0:TCTACGCA+GGCTATTG ptg000093l 2 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2477:39508:8230_1:N:0:TCTACGCA+GGCTATTG ptg000045l 57985 Chromosomal sequence could not be extracted for LH00652:104:22KG7JLT4:8:2477:39500:8244_1:N:0:TCTACGCA+GGCTATTG ptg000045l 57985 33813626 reads; of these: 33813626 (100.00%) were paired; of these: 13307433 (39.36%) aligned concordantly 0 times 6977156 (20.63%) aligned concordantly exactly 1 time 13529037 (40.01%) aligned concordantly >1 times 60.64% overall alignment rate 33813626 reads; of these: 33813626 (100.00%) were paired; of these: 13302269 (39.34%) aligned concordantly 0 times 6977572 (20.64%) aligned concordantly exactly 1 time 13533785 (40.02%) aligned concordantly >1 times 60.66% overall alignment rate Processed 33813626 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 135254504. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 135254504. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 135254504. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 135254504. Successfully deleted the temporary files 2A3_R1_001.fastp-trim.fq.gz_C_to_T.fastq and 2A3_R2_001.fastp-trim.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 33813626 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1004090510 Total methylated C's in CpG context: 17669415 Total methylated C's in CHG context: 978757 Total methylated C's in CHH context: 3984787 Total methylated C's in Unknown context: 54365 Total unmethylated C's in CpG context: 135626741 Total unmethylated C's in CHG context: 168862827 Total unmethylated C's in CHH context: 676967983 Total unmethylated C's in Unknown context: 2649252 C methylated in CpG context: 11.5% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in unknown context (CN or CHN): 2.0% Bismark completed in 0d 2h 22m 14s ==================== Bismark run complete ====================