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/1A10_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/1A10_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/1A10_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/1A10_R2_001.fastp-trim.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file 1A10_R1_001.fastp-trim.fq.gz to 1A10_R1_001.fastp-trim.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file 1A10_R1_001.fastp-trim.fq.gz (41468675 sequences in total) Writing a G -> A converted version of the input file 1A10_R2_001.fastp-trim.fq.gz to 1A10_R2_001.fastp-trim.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file 1A10_R2_001.fastp-trim.fq.gz (41468675 sequences in total) Input files are 1A10_R1_001.fastp-trim.fq.gz_C_to_T.fastq and 1A10_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 1A10_R1_001.fastp-trim.fq.gz_C_to_T.fastq and 1A10_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: LH00526:197:22KFKVLT4:3:1101:50282:1056_1:N:0:AGCCTATC+GTTACGCA/1 99 ptg000018l_CT_converted 14440089 42 125M = 14440386 422 GTGATGTTGAGTTGTTTGTGGTAAAATAGGGATTTTAGTAAGTATGGTTGAGGTTAGTGATAGATATGGATAGTAATGTGGATGAAATTAGTGGTATTATGGTTATGATTGTATAAAGTAAAGTA IIIII9IIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIII9IIIIIIIIII9IIIIIIIIIIIIIIIII9I-IIIIIIIIII9IIIIIIIIIIII9II9IIIIII9IIIIIIII9III AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:125 YS:i:-6 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:50282:1056_2:N:0:AGCCTATC+GTTACGCA/2 147 ptg000018l_CT_converted 14440386 42 125M = 14440089 -422 AATTGATTTTGGTGAATGTAGAATGTAAATTAAGGTATTAGTGAGATATTAATGATATTTATATTAAATAGTATGATTATATATTTGAGAATGGATTAATTTTATGTTGTGATTTTTAAAAAAGA -III-9IIIIIII9I-----II-9III-I9IIIIII9II-III99IIII9I-II99IIII-IIIIIIIIIII9I9III-I9III-IIII-II999IIIII9-9IIII9II-IIIIII9I9IIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:110T14 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1A10_R1_001.fastp-trim.fq.gz_C_to_T.fastq and 1A10_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: LH00526:197:22KFKVLT4:3:1101:50282:1056_1:N:0:AGCCTATC+GTTACGCA/1 77 * 0 0 * * 0 0 GTGATGTTGAGTTGTTTGTGGTAAAATAGGGATTTTAGTAAGTATGGTTGAGGTTAGTGATAGATATGGATAGTAATGTGGATGAAATTAGTGGTATTATGGTTATGATTGTATAAAGTAAAGTA IIIII9IIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIII9IIIIIIIIII9IIIIIIIIIIIIIIIII9I-IIIIIIIIII9IIIIIIIIIIII9II9IIIIII9IIIIIIII9III YT:Z:UP LH00526:197:22KFKVLT4:3:1101:50282:1056_2:N:0:AGCCTATC+GTTACGCA/2 141 * 0 0 * * 0 0 TCTTTTTTAAAAATCACAACATAAAATTAATCCATTCTCAAATATATAATCATACTATTTAATATAAATATCATTAATATCTCACTAATACCTTAATTTACATTCTACATTCACCAAAATCAATT IIIII9I9IIIIII-II9IIII9-9IIIII999II-IIII-III9I-III9I9IIIIIIIIIII-IIII99II-I9IIII99III-II9IIIIII9I-III9-II-----I9IIIIIII9-III- YT:Z:UP >>> Writing bisulfite mapping results to 1A10_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/1A10_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/1A10_R2_001.fastp-trim.fq.gz Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1125:25544:19588_1:N:0:AGCCTATC+GTTACGCA ptg000113l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1125:25560:19588_1:N:0:AGCCTATC+GTTACGCA ptg000113l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1125:25552:19602_1:N:0:AGCCTATC+GTTACGCA ptg000113l 1 Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1140:30593:5693_1:N:0:AGCCTATC+GTTACGCA ptg000096l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1157:3800:22572_1:N:0:AGCCTATC+GTTACGCA ptg000048l 1 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1176:20413:28553_1:N:0:AGCCTATC+GTTACGCA ptg000127l 2 Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1205:51997:7444_1:N:0:AGCCTATC+GTTACGCA ptg000092l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1211:32268:23160_1:N:0:AGCCTATC+GTTACGCA ptg000114l 51144 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1220:14773:21788_1:N:0:AGCCTATC+GTTACGCA ptg000127l 1 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1238:7708:14349_1:N:0:AGCCTATC+GTTACGCA ptg000045l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1239:48566:18538_1:N:0:AGCCTATC+GTTACGCA ptg000121l 50753 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1242:24832:26760_1:N:0:AGCCTATC+GTTACGCA ptg000125l 18902 Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1268:46171:19742_1:N:0:AGCCTATC+GTTACGCA ptg000121l 50751 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1275:33353:8368_1:N:0:AGCCTATC+GTTACGCA ptg000107l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1297:37326:13341_1:N:0:AGCCTATC+GTTACGCA ptg000094l 2 Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1301:51220:15204_1:N:0:AGCCTATC+GTTACGCA ptg000125l 18896 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1329:11973:11394_1:N:0:AGCCTATC+GTTACGCA ptg000074l 12236 Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1344:31354:9447_1:N:0:AGCCTATC+GTTACGCA ptg000024l 3 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1357:41526:3942_1:N:0:AGCCTATC+GTTACGCA ptg000045l 57984 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1357:37188:18650_1:N:0:AGCCTATC+GTTACGCA ptg000077l 42482 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1358:22355:11492_1:N:0:AGCCTATC+GTTACGCA ptg000088l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1363:6147:21984_1:N:0:AGCCTATC+GTTACGCA ptg000096l 56417 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1365:8841:26760_1:N:0:AGCCTATC+GTTACGCA ptg000096l 1 Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1378:11925:5791_1:N:0:AGCCTATC+GTTACGCA ptg000088l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1387:37666:13173_1:N:0:AGCCTATC+GTTACGCA ptg000093l 36777 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1396:27340:6001_1:N:0:AGCCTATC+GTTACGCA ptg000092l 1 Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1422:36088:6463_1:N:0:AGCCTATC+GTTACGCA ptg000048l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1423:49893:10413_1:N:0:AGCCTATC+GTTACGCA ptg000047l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1424:21101:22068_1:N:0:AGCCTATC+GTTACGCA ntLink_0 96490 Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1444:24419:13915_1:N:0:AGCCTATC+GTTACGCA ptg000092l 28981 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1447:5192:19939_1:N:0:AGCCTATC+GTTACGCA ptg000160l 32573 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1457:7911:13467_1:N:0:AGCCTATC+GTTACGCA ptg000160l 32581 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1457:7919:13481_1:N:0:AGCCTATC+GTTACGCA ptg000117l 29992 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1466:30391:21591_1:N:0:AGCCTATC+GTTACGCA ptg000101l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1467:2465:17823_1:N:0:AGCCTATC+GTTACGCA ptg000057l 39958 Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1474:48137:26144_1:N:0:AGCCTATC+GTTACGCA ptg000123l 44473 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1479:28287:1448_1:N:0:AGCCTATC+GTTACGCA ptg000093l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1488:18479:15204_1:N:0:AGCCTATC+GTTACGCA ptg000101l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1489:2408:25906_1:N:0:AGCCTATC+GTTACGCA ptg000115l 1 Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2108:43387:28091_1:N:0:AGCCTATC+GTTACGCA ptg000011l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2121:14037:29534_1:N:0:AGCCTATC+GTTACGCA ptg000098l 55094 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2146:43808:22348_1:N:0:AGCCTATC+GTTACGCA ptg000182l 35544 Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2162:38880:18188_1:N:0:AGCCTATC+GTTACGCA ptg000004l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2175:14344:27657_1:N:0:AGCCTATC+GTTACGCA ptg000048l 76450 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2178:15776:13411_1:N:0:AGCCTATC+GTTACGCA ptg000004l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2178:15760:13439_1:N:0:AGCCTATC+GTTACGCA ptg000004l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2186:39802:7402_1:N:0:AGCCTATC+GTTACGCA ptg000011l 2 Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2196:32204:14083_1:N:0:AGCCTATC+GTTACGCA ptg000077l 42496 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2201:37876:23062_1:N:0:AGCCTATC+GTTACGCA ptg000094l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2210:33417:6407_1:N:0:AGCCTATC+GTTACGCA ptg000101l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2210:33409:6421_1:N:0:AGCCTATC+GTTACGCA ptg000101l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2219:24435:17137_1:N:0:AGCCTATC+GTTACGCA ptg000098l 55097 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2219:24411:17151_1:N:0:AGCCTATC+GTTACGCA ptg000098l 55097 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2232:39697:6491_1:N:0:AGCCTATC+GTTACGCA ptg000092l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2233:31241:11380_1:N:0:AGCCTATC+GTTACGCA ptg000092l 1 Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2246:11657:23819_1:N:0:AGCCTATC+GTTACGCA ptg000144l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2259:45799:15092_1:N:0:AGCCTATC+GTTACGCA ptg000121l 50744 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2262:30100:6575_1:N:0:AGCCTATC+GTTACGCA ptg000102l 1 Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2289:34575:7794_1:N:0:AGCCTATC+GTTACGCA ptg000101l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2290:20203:5777_1:N:0:AGCCTATC+GTTACGCA ptg000101l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2292:35958:29072_1:N:0:AGCCTATC+GTTACGCA ptg000117l 30005 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2310:19321:16829_1:N:0:AGCCTATC+GTTACGCA ptg000008l 2 Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2349:3832:23384_1:N:0:AGCCTATC+GTTACGCA ptg000053l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2351:32341:3031_1:N:0:AGCCTATC+GTTACGCA ptg000105l 83217 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2351:32357:3031_1:N:0:AGCCTATC+GTTACGCA ptg000105l 83217 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2356:9246:5693_1:N:0:AGCCTATC+GTTACGCA ptg000048l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2366:14085:23370_1:N:0:AGCCTATC+GTTACGCA ptg000101l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2369:39123:10679_1:N:0:AGCCTATC+GTTACGCA ptg000055l 50528 Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2408:38095:12038_1:N:0:AGCCTATC+GTTACGCA ptg000106l 40366 Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2426:25042:22082_1:N:0:AGCCTATC+GTTACGCA ptg000092l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2451:26507:23496_1:N:0:AGCCTATC+GTTACGCA ptg000057l 2 Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2468:50201:7752_1:N:0:AGCCTATC+GTTACGCA ptg000096l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2469:47037:8578_1:N:0:AGCCTATC+GTTACGCA ptg000098l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2480:6859:6043_1:N:0:AGCCTATC+GTTACGCA ptg000092l 1 Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1129:21619:2569_1:N:0:AGCCTATC+GTTACGCA ptg000115l 1 Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1148:46041:22152_1:N:0:AGCCTATC+GTTACGCA ptg000024l 3 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1152:21312:15820_1:N:0:AGCCTATC+GTTACGCA ptg000113l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1155:46640:23356_1:N:0:AGCCTATC+GTTACGCA ptg000045l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1169:3144:21381_1:N:0:AGCCTATC+GTTACGCA ptg000092l 2 Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1181:26167:21956_1:N:0:AGCCTATC+GTTACGCA ptg000077l 42482 Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1233:44043:15218_1:N:0:AGCCTATC+GTTACGCA ntLink_0 96490 Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1250:17225:23230_1:N:0:AGCCTATC+GTTACGCA ptg000113l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1273:17654:15680_1:N:0:AGCCTATC+GTTACGCA ptg000092l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1273:17646:15694_1:N:0:AGCCTATC+GTTACGCA ptg000092l 1 Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1287:27988:26228_1:N:0:AGCCTATC+GTTACGCA ptg000048l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1291:32535:25976_1:N:0:AGCCTATC+GTTACGCA ptg000027l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1291:32527:25990_1:N:0:AGCCTATC+GTTACGCA ptg000027l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1301:35521:20079_1:N:0:AGCCTATC+GTTACGCA ptg000004l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1306:33782:11604_1:N:0:AGCCTATC+GTTACGCA ptg000063l 30368 Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1317:24144:11030_1:N:0:AGCCTATC+GTTACGCA ptg000130l 35810 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1327:52094:8592_1:N:0:AGCCTATC+GTTACGCA ptg000048l 1 Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1355:40620:13467_1:N:0:AGCCTATC+GTTACGCA ptg000066l 66380 Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1378:22283:27335_1:N:0:AGCCTATC+GTTACGCA ptg000093l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1382:20211:5006_1:N:0:AGCCTATC+GTTACGCA ptg000098l 55086 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1398:42052:29142_1:N:0:AGCCTATC+GTTACGCA ptg000053l 71540 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1404:6608:21437_1:N:0:AGCCTATC+GTTACGCA ptg000093l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1408:3266:25402_1:N:0:AGCCTATC+GTTACGCA ptg000121l 50742 Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1414:2667:3045_1:N:0:AGCCTATC+GTTACGCA ptg000096l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1420:33110:5959_1:N:0:AGCCTATC+GTTACGCA ptg000025l 1 Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1451:39058:7654_1:N:0:AGCCTATC+GTTACGCA ptg000117l 30013 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1455:51746:25780_1:N:0:AGCCTATC+GTTACGCA ptg000115l 42042 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1455:51738:25794_1:N:0:AGCCTATC+GTTACGCA ptg000115l 42042 Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1489:25778:10525_1:N:0:AGCCTATC+GTTACGCA ptg000146l 38997 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1492:33231:13285_1:N:0:AGCCTATC+GTTACGCA ptg000113l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1492:33239:13299_1:N:0:AGCCTATC+GTTACGCA ptg000113l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1493:51690:10581_1:N:0:AGCCTATC+GTTACGCA ptg000125l 18889 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1494:27389:20989_1:N:0:AGCCTATC+GTTACGCA ptg000092l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1497:12378:27082_1:N:0:AGCCTATC+GTTACGCA ptg000169l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2108:46843:23987_1:N:0:AGCCTATC+GTTACGCA ptg000015l 14997104 Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2121:15226:29688_1:N:0:AGCCTATC+GTTACGCA ptg000093l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2130:19386:22460_1:N:0:AGCCTATC+GTTACGCA ptg000106l 40365 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2160:16982:4824_1:N:0:AGCCTATC+GTTACGCA ptg000092l 1 Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2174:48404:13187_1:N:0:AGCCTATC+GTTACGCA ptg000113l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2174:17961:27867_1:N:0:AGCCTATC+GTTACGCA ptg000048l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2184:16043:11352_1:N:0:AGCCTATC+GTTACGCA ptg000125l 18900 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2198:33960:2135_1:N:0:AGCCTATC+GTTACGCA ptg000055l 2 Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2206:46535:11296_1:N:0:AGCCTATC+GTTACGCA ptg000092l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2237:13697:29254_1:N:0:AGCCTATC+GTTACGCA ptg000128l 44515 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2247:25147:25990_1:N:0:AGCCTATC+GTTACGCA ptg000093l 36783 Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2257:28748:26032_1:N:0:AGCCTATC+GTTACGCA ptg000011l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2268:9189:3746_1:N:0:AGCCTATC+GTTACGCA ptg000066l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2269:40984:10623_1:N:0:AGCCTATC+GTTACGCA ptg000092l 28993 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2281:13478:13495_1:N:0:AGCCTATC+GTTACGCA ptg000063l 30354 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2281:21619:25962_1:N:0:AGCCTATC+GTTACGCA ptg000092l 1 Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2323:50144:1322_1:N:0:AGCCTATC+GTTACGCA ntLink_0 96467 Processed 38000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2340:38071:22082_1:N:0:AGCCTATC+GTTACGCA ptg000039l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2340:38079:22096_1:N:0:AGCCTATC+GTTACGCA ptg000039l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2344:48744:20807_1:N:0:AGCCTATC+GTTACGCA ptg000092l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2349:6001:9545_1:N:0:AGCCTATC+GTTACGCA ptg000075l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2357:39891:5679_1:N:0:AGCCTATC+GTTACGCA ptg000025l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2379:36994:1476_1:N:0:AGCCTATC+GTTACGCA ptg000066l 66388 Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2461:37310:24463_1:N:0:AGCCTATC+GTTACGCA ptg000133l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2465:39074:22026_1:N:0:AGCCTATC+GTTACGCA ptg000113l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2465:39090:22026_1:N:0:AGCCTATC+GTTACGCA ptg000113l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2479:20988:19210_1:N:0:AGCCTATC+GTTACGCA ptg000011l 1 Processed 41000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2484:22809:16002_1:N:0:AGCCTATC+GTTACGCA ptg000113l 1 41468675 reads; of these: 41468675 (100.00%) were paired; of these: 16280072 (39.26%) aligned concordantly 0 times 8279096 (19.96%) aligned concordantly exactly 1 time 16909507 (40.78%) aligned concordantly >1 times 60.74% overall alignment rate 41468675 reads; of these: 41468675 (100.00%) were paired; of these: 16289847 (39.28%) aligned concordantly 0 times 8280083 (19.97%) aligned concordantly exactly 1 time 16898745 (40.75%) aligned concordantly >1 times 60.72% overall alignment rate Processed 41468675 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 165874700. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 165874700. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 165874700. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 165874700. Successfully deleted the temporary files 1A10_R1_001.fastp-trim.fq.gz_C_to_T.fastq and 1A10_R2_001.fastp-trim.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 41468675 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1197362045 Total methylated C's in CpG context: 19694599 Total methylated C's in CHG context: 1240696 Total methylated C's in CHH context: 5069102 Total methylated C's in Unknown context: 62791 Total unmethylated C's in CpG context: 165078427 Total unmethylated C's in CHG context: 200543012 Total unmethylated C's in CHH context: 805736209 Total unmethylated C's in Unknown context: 3198095 C methylated in CpG context: 10.7% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in unknown context (CN or CHN): 1.9% Bismark completed in 0d 2h 48m 28s ==================== Bismark run complete ====================