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/94M_R1.fastp-trim.fq.gz ../data/94M_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/94M_R1.fastp-trim.fq.gz and ../data/94M_R2.fastp-trim.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file 94M_R1.fastp-trim.fq.gz to 94M_R1.fastp-trim.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file 94M_R1.fastp-trim.fq.gz (94561401 sequences in total) Writing a G -> A converted version of the input file 94M_R2.fastp-trim.fq.gz to 94M_R2.fastp-trim.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file 94M_R2.fastp-trim.fq.gz (94561401 sequences in total) Input files are 94M_R1.fastp-trim.fq.gz_C_to_T.fastq and 94M_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 94M_R1.fastp-trim.fq.gz_C_to_T.fastq and 94M_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: LH00469:254:22HGFVLT4:2:1101:3840:1014_1:N:0:ACTGAGGT+GTCAACAG/1 99 NC_086380.1_CT_converted 47138855 1 108M = 47138835 -128 GGTAAAAATTGGGTATTTAAAATTAAGGTTGATTTTAATATGTTTAATATGTTGTTGGTATTTTTTTGGTTAAATTATTTTTTATATAAAATTTTAATTTTTTTTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-30 XS:i:-30 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:98G1G0A1G1A2 YS:i:-6 YT:Z:CP LH00469:254:22HGFVLT4:2:1101:3840:1014_2:N:0:ACTGAGGT+GTCAACAG/2 147 NC_086380.1_CT_converted 47138835 1 108M = 47138855 128 TTTGTAGATAGAATTTATGTGGTAAAAATTGGGTATTTAAAATTAAGGTTGATTTTAATATGTTTAATATGTTGTTGGTATTTTTTTGGTTAAATTATTTTTTATATA IIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:14G93 YS:i:-30 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 94M_R1.fastp-trim.fq.gz_C_to_T.fastq and 94M_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: LH00469:254:22HGFVLT4:2:1101:3840:1014_1:N:0:ACTGAGGT+GTCAACAG/1 83 NC_086380.1_GA_converted 49966589 6 108M = 49966609 128 AAAAAAAAAAATTAAAATTTTATATAAAAAATAATTTAACCAAAAAAATACCAACAACATATTAAACATATTAAAATCAACCTTAATTTTAAATACCCAATTTTTACC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-30 XS:i:-30 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:2T1C1T0C1C98 YS:i:0 YT:Z:CP LH00469:254:22HGFVLT4:2:1101:3840:1014_2:N:0:ACTGAGGT+GTCAACAG/2 163 NC_086380.1_GA_converted 49966609 6 108M = 49966589 -128 TATATAAAAAATAATTTAACCAAAAAAATACCAACAACATATTAAACATATTAAAATCAACCTTAATTTTAAATACCCAATTTTTACCACATAAATTCTATCTACAAA IIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:108 YS:i:-30 YT:Z:CP >>> Writing bisulfite mapping results to 94M_pe.bam <<< Reading in the sequence files ../data/94M_R1.fastp-trim.fq.gz and ../data/94M_R2.fastp-trim.fq.gz Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1103:33045:7051_1:N:0:ACTGAGGT+GTCAACAG NW_026963536.1 19405 Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1110:34049:14167_1:N:0:ACTGAGGT+GTCAACAG NW_026963717.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1115:37245:9587_1:N:0:ACTGAGGT+GTCAACAG NW_026963613.1 1 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1120:17945:13159_1:N:0:ACTGAGGT+GTCAACAG NW_026963303.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1123:25617:9265_1:N:0:ACTGAGGT+GTCAACAG NW_026963585.1 2 Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1133:12386:26760_1:N:0:ACTGAGGT+GTCAACAG NW_026963755.1 1 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1139:2837:13397_1:N:0:ACTGAGGT+GTCAACAG NW_026963333.1 249885 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1139:48898:20261_1:N:0:ACTGAGGT+GTCAACAG NW_026963737.1 15373 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1141:44302:22502_1:N:0:ACTGAGGT+GTCAACAG NW_026963415.1 2 Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1148:21813:6967_1:N:0:ACTGAGGT+GTCAACAG NW_026963316.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1149:11463:20513_1:N:0:AATGAGGT+GTCAACAG NW_026963585.1 1 Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1159:12515:10315_1:N:0:ACTGAGGT+GTCAACAG NW_026963315.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1163:38847:23202_1:N:0:ACTGAGGT+GTCAACAG NW_026963774.1 18492 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1163:34882:25472_1:N:0:ACTGAGGT+GTCAACAG NW_026963700.1 32484 Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1174:39292:14588_1:N:0:ACTGAGGT+GTCAACAG NW_026963616.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1174:39268:14602_1:N:0:ACTGAGGT+GTCAACAG NW_026963616.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1174:39284:14630_1:N:0:ACTGAGGT+GTCAACAG NW_026963616.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1180:10468:24001_1:N:0:ACTGAGGT+GTCAACAG NW_026963305.1 1249871 Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1197:15105:19560_1:N:0:ACTGAGGT+GTCAACAG NW_026963372.1 501136 Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1221:2028:8214_1:N:0:AATGAGGT+GTCAACAG NW_026963585.1 2 Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1232:32398:1953_1:N:0:ACTGAGGT+GTCAACAG NW_026963733.1 30552 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1233:48890:23721_1:N:0:ACTGAGGT+GTCAACAG NW_026963598.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1233:48882:23735_1:N:0:ACTGAGGT+GTCAACAG NW_026963598.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1236:11471:23721_1:N:0:ACTGAGGT+GTCAACAG NW_026963673.1 26164 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1236:11471:23749_1:N:0:ACTGAGGT+GTCAACAG NW_026963673.1 26164 Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1267:37035:6701_1:N:0:ACTGAGGT+GTCAACAG NW_026963402.1 95206 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1270:33952:18286_1:N:0:AATGAGGT+GTCAACAG NW_026963345.1 224368 Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1280:39851:9251_1:N:0:ACTGAGGT+GTCAACAG NW_026963747.1 21180 Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1292:1186:3647_1:N:0:ACTGAGGT+GTCAACAG NW_026963326.1 1 Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1295:44747:15736_1:N:0:ACTGAGGT+GTCAACAG NW_026963389.1 32298 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1297:45556:8956_1:N:0:ACTGAGGT+GTCAACAG NW_026963791.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1304:40935:18916_1:N:0:ACTGAGGT+GTCAACAG NW_026963736.1 25932 Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1306:15558:2723_1:N:0:ACTGAGGT+GTCAACAG NW_026963631.1 26277 Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1323:49335:25556_1:N:0:ACTGAGGT+GTCAACAG NW_026963511.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1324:38775:20975_1:N:0:ACTGAGGT+GTCAACAG NW_026963415.1 3 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1325:23699:25163_1:N:0:ACTGAGGT+GTCAACAG NW_026963769.1 19028 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1329:30844:28427_1:N:0:ACTGAGGT+GTCAACAG NW_026963609.1 1 Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1333:47935:10329_1:N:0:ACTGAGGT+GTCAACAG NW_026963740.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1339:32179:28385_1:N:0:AATGAGGT+GTCAACAG NW_026963585.1 2 Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1348:34631:3381_1:N:0:ACTGAGGT+GTCAACAG NW_026963738.1 1 Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1354:9594:6771_1:N:0:ACTGAGGT+GTCAACAG NW_026963372.1 501136 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1358:51512:18454_1:N:0:ACTGAGGT+GTCAACAG NW_026963415.1 1 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 LH00469:254:22HGFVLT4:2:1381:10152:23791_1:N:0:ACTGAGGT+GTCAACAG NW_026963778.1 3 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1385:15485:22124_1:N:0:ACTGAGGT+GTCAACAG NW_026963602.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1388:42513:12038_1:N:0:ACTGAGGT+GTCAACAG NW_026963789.1 26200 Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1395:12337:1939_1:N:0:ACTGAGGT+GTCAACAG NW_026963511.1 1 Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1403:8121:9012_1:N:0:ACTGAGGT+GTCAACAG NW_026963462.1 16216 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1403:8097:9026_1:N:0:ACTGAGGT+GTCAACAG NW_026963462.1 16216 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1403:15202:10483_1:N:0:ACTGAGGT+GTCAACAG NW_026963791.1 2 Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1410:30529:22978_1:N:0:ACTGAGGT+GTCAACAG NW_026963328.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1417:31152:11114_1:N:0:ACTGAGGT+GTCAACAG NW_026963334.1 1 Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1420:21959:15176_1:N:0:ACTGAGGT+GTCAACAG NW_026963678.1 25861 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1425:10096:3661_1:N:0:ACTGAGGT+GTCAACAG NW_026963317.1 4467314 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1425:10104:3675_1:N:0:ACTGAGGT+GTCAACAG NW_026963317.1 4467314 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1428:37901:2429_1:N:0:ACTGAGGT+GTCAACAG NW_026963740.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1428:37909:2443_1:N:0:ACTGAGGT+GTCAACAG NW_026963740.1 1 Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1431:2028:9895_1:N:0:ACTGAGGT+GTCAACAG NW_026963299.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1431:50889:13873_1:N:0:ACTGAGGT+GTCAACAG NW_026963393.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1436:26393:13635_1:N:0:AATGAGGT+GTCAACAG NW_026963415.1 3 Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1438:42052:2555_1:N:0:ACTGAGGT+GTCAACAG NW_026963402.1 95217 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1445:37682:8466_1:N:0:ACTGAGGT+GTCAACAG NW_026963630.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1445:37706:8480_1:N:0:ACTGAGGT+GTCAACAG NW_026963630.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1445:37698:8494_1:N:0:ACTGAGGT+GTCAACAG NW_026963630.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1446:16553:18986_1:N:0:AATGAGGT+GTCAACAG NW_026963634.1 1 Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1450:23496:15344_1:N:0:ACTGAGGT+GTCAACAG NW_026963425.1 28463 Processed 38000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1458:20114:7219_1:N:0:AATGAGGT+GTCAACAG NW_026963291.1 1 Processed 39000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1471:14409:15946_1:N:0:AATGAGGT+GTCAACAG NW_026963789.1 26199 Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1488:15072:4208_1:N:0:ACTGAGGT+GTCAACAG NW_026963362.1 2 Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1497:15267:28777_1:N:0:ACTGAGGT+GTCAACAG NW_026963348.1 1 Processed 43000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2107:15250:8774_1:N:0:ACTGAGGT+GTCAACAG NW_026963348.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2107:15267:8774_1:N:0:ACTGAGGT+GTCAACAG NW_026963501.1 19453 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2107:15283:8774_1:N:0:ACTGAGGT+GTCAACAG NW_026963348.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2107:15299:8774_1:N:0:ACTGAGGT+GTCAACAG NW_026963348.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2107:15275:8788_1:N:0:ACTGAGGT+GTCAACAG NW_026963348.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2111:13017:18664_1:N:0:ACTGAGGT+GTCAACAG NW_026963482.1 3 Processed 44000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2119:17743:8550_1:N:0:ACTGAGGT+GTCAACAG NW_026963585.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2120:8987:23230_1:N:0:AATGAGGT+GTCAACAG NW_026963415.1 2 Processed 45000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2129:11277:22600_1:N:0:ACTGAGGT+GTCAACAG NW_026963377.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2130:25722:25191_1:N:0:ACTGAGGT+GTCAACAG NW_026963585.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2132:45977:11478_1:N:0:ACTGAGGT+GTCAACAG NW_026963443.1 56336 Processed 46000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2137:5402:15232_1:N:0:ACTGAGGT+GTCAACAG NC_007687.1 18558 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2139:38791:21647_1:N:0:ACTGAGGT+GTCAACAG NW_026963684.1 18474 Processed 47000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2146:25973:9657_1:N:0:ACTGAGGT+GTCAACAG NW_026963422.1 18067 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2148:4892:22894_1:N:0:ACTGAGGT+GTCAACAG NW_026963415.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2152:30213:7332_1:N:0:ACTGAGGT+GTCAACAG NW_026963415.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2154:21417:4432_1:N:0:ACTGAGGT+GTCAACAG NW_026963415.1 2 Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2167:37731:27125_1:N:0:ACTGAGGT+GTCAACAG NC_007687.1 18532 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2170:19305:16409_1:N:0:AATGAGGT+GTCAACAG NW_026963415.1 3 Processed 50000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2178:32123:17221_1:N:0:ACTGAGGT+GTCAACAG NW_026963443.1 1 Processed 51000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2186:17678:20485_1:N:0:AATGAGGT+GTCAACAG NW_026963291.1 2 Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2206:32770:16829_1:N:0:ACTGAGGT+GTCAACAG NW_026963415.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2206:32778:16843_1:N:0:ACTGAGGT+GTCAACAG NW_026963415.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2206:25730:25177_1:N:0:ACTGAGGT+GTCAACAG NW_026963757.1 1 Processed 54000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2220:38831:1714_1:N:0:ACTGCGGT+GTCAACAG NW_026963740.1 1 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 LH00469:254:22HGFVLT4:2:2250:35206:15386_1:N:0:ACTGAGGT+GTCAACAG NW_026963345.1 224368 Processed 58000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2257:29598:27559_1:N:0:ACTGAGGT+GTCAACAG NW_026963585.1 49252 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2258:50970:23875_1:N:0:ACTGAGGT+GTCAACAG NW_026963645.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2261:46745:14770_1:N:0:ACTGAGGT+GTCAACAG NW_026963586.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2265:9286:20555_1:N:0:ACTGAGGT+GTCAACAG NW_026963319.1 249900 Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2281:12952:3900_1:N:0:ACTGAGGT+GTCAACAG NW_026963372.1 501141 Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2301:28845:4376_1:N:0:ACTGAGGT+GTCAACAG NW_026963389.1 32297 Processed 63000000 sequence pairs so far Processed 64000000 sequence pairs so far Processed 65000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2328:30755:7486_1:N:0:ACTGAGGT+GTCAACAG NW_026963348.1 21700 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2335:31257:5833_1:N:0:AATGAGGT+GTCAACAG NW_026963789.1 26200 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2337:9060:1028_1:N:0:ACTGAGGT+GTCAACAG NW_026963809.1 20318 Processed 66000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2339:3630:26256_1:N:0:ACTGAGGT+GTCAACAG NW_026963640.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2339:3646:26256_1:N:0:ACTGAGGT+GTCAACAG NW_026963640.1 1 Processed 67000000 sequence pairs so far Processed 68000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2361:26660:3059_1:N:0:ACTGAGGT+GTCAACAG NW_026963446.1 2 Processed 69000000 sequence pairs so far Processed 70000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2381:40749:7724_1:N:0:ACTGAGGT+GTCAACAG NW_026963443.1 56357 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2384:5766:26340_1:N:0:ACTGAGGT+GTCAACAG NW_026963402.1 95210 Processed 71000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2396:23116:25724_1:N:0:ACTGAGGT+GTCAACAG NW_026963683.1 23732 Processed 72000000 sequence pairs so far Processed 73000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2421:15712:7416_1:N:0:ACTGAGGT+GTCAACAG NW_026963377.1 15232 Processed 74000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2424:14150:10539_1:N:0:AATGAGGT+GTCAACAG NW_026963734.1 3 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2427:20373:1196_1:N:0:ACTGAGGT+GTCAACAG NW_026963587.1 24411 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2434:30075:3535_1:N:0:ACTGAGGT+GTCAACAG NW_026963415.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2434:7708:3732_1:N:0:AATGAGGT+GTCAACAG NW_026963677.1 25135 Processed 75000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2434:27502:11044_1:N:0:AATGAGGT+GTCAACAG NW_026963789.1 26197 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2438:36930:7332_1:N:0:ACTGAGGT+GTCAACAG NW_026963393.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2438:36954:7346_1:N:0:ACTGAGGT+GTCAACAG NW_026963393.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2438:36970:7346_1:N:0:ACTGAGGT+GTCAACAG NW_026963393.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2439:43144:16184_1:N:0:ACTGAGGT+GTCAACAG NW_026963585.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2439:43161:16184_1:N:0:ACTGAGGT+GTCAACAG NW_026963585.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2441:12361:4838_1:N:0:AATGAGGT+GTCAACAG NW_026963755.1 23836 Processed 76000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2450:16238:3928_1:N:0:ACTGAGGT+GTCAACAG NW_026963689.1 2 Processed 77000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2463:14093:13747_1:N:0:ACTGAGGT+GTCAACAG NW_026963765.1 26759 Processed 78000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2470:20162:7472_1:N:0:AATGAGGT+GTCAACAG NW_026963415.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2474:21166:24421_1:N:0:ACTGAGGT+GTCAACAG NW_026963480.1 2 Processed 79000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2481:15946:11884_1:N:0:ACTGAGGT+GTCAACAG NW_026963598.1 29323 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2481:15954:11898_1:N:0:ACTGAGGT+GTCAACAG NW_026963598.1 29323 Processed 80000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2488:24168:12080_1:N:0:ACTGAGGT+GTCAACAG NW_026963677.1 25109 Processed 81000000 sequence pairs so far Processed 82000000 sequence pairs so far Processed 83000000 sequence pairs so far Processed 84000000 sequence pairs so far Processed 85000000 sequence pairs so far Processed 86000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1428:40150:25177_1:N:0:ACTGAGGT+GTCAACAG NW_026963416.1 2 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 LH00586:122:22HTFTLT4:7:2173:34906:9629_1:N:0:ACTGAGGT+GTCAACAG NW_026963418.1 81305 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2218:31532:5973_1:N:0:ACTGAGGT+GTCAACAG NW_026963585.1 49252 Processed 90000000 sequence pairs so far Processed 91000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2327:6454:5539_1:N:0:ACTGAGGT+GTCAACAG NW_026963315.1 1 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2347:26741:21409_1:N:0:ACTGAGGT+GTCAACAG NW_026963677.1 25109 Processed 92000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2367:36654:12514_1:N:0:ACTGAGGT+GTCAACAG NW_026963415.1 2 Processed 93000000 sequence pairs so far Processed 94000000 sequence pairs so far 94561401 reads; of these: 94561401 (100.00%) were paired; of these: 38464198 (40.68%) aligned concordantly 0 times 17499473 (18.51%) aligned concordantly exactly 1 time 38597730 (40.82%) aligned concordantly >1 times 59.32% overall alignment rate 94561401 reads; of these: 94561401 (100.00%) were paired; of these: 38472542 (40.69%) aligned concordantly 0 times 17492587 (18.50%) aligned concordantly exactly 1 time 38596272 (40.82%) aligned concordantly >1 times 59.31% overall alignment rate Processed 94561401 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 378245604. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 378245604. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 378245604. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 378245604. Successfully deleted the temporary files 94M_R1.fastp-trim.fq.gz_C_to_T.fastq and 94M_R2.fastp-trim.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 94561401 Final Cytosine Methylation Report ================================= Total number of C's analysed: 2311096675 Total methylated C's in CpG context: 31882271 Total methylated C's in CHG context: 3604652 Total methylated C's in CHH context: 16559906 Total methylated C's in Unknown context: 420834 Total unmethylated C's in CpG context: 248769836 Total unmethylated C's in CHG context: 372281874 Total unmethylated C's in CHH context: 1637998136 Total unmethylated C's in Unknown context: 12697706 C methylated in CpG context: 11.4% C methylated in CHG context: 1.0% C methylated in CHH context: 1.0% C methylated in unknown context (CN or CHN): 3.2% Bismark completed in 0d 6h 31m 25s ==================== Bismark run complete ==================== Unable to flush stdout: Broken pipe