Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.5.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/srlab/programs/samtools-1.20/samtools' Reference genome folder provided is ../output/01-bismark-init/ (absolute path is '/gscratch/scrubbed/sr320/github/project-mytilus-methylation/output/01-bismark-init/)' FastQ format assumed (by default) Attention: early reports suggested that high values of -p to have diminishing returns. Please test different values using a small subset of data for your hardware setting. 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 '/gscratch/scrubbed/sr320/github/project-mytilus-methylation/code'): ../data/raw-wgbs/242M_1.fastq.gz ../data/raw-wgbs/242M_2.fastq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Output will be written into the directory: /gscratch/scrubbed/sr320/github/project-mytilus-methylation/output/01-bismark-init/ Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/github/project-mytilus-methylation/code Now reading in and storing sequence information of the genome specified in: /gscratch/scrubbed/sr320/github/project-mytilus-methylation/output/01-bismark-init/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are ../data/raw-wgbs/242M_1.fastq.gz and ../data/raw-wgbs/242M_2.fastq.gz Input files are in FastQ format Writing a C -> T converted version of the input file 242M_1.fastq.gz to 242M_1.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 242M_1.fastq.gz to 242M_1.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 242M_1.fastq.gz (86793768 sequences in total) Writing a C -> T converted version of the input file 242M_2.fastq.gz to 242M_2.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 242M_2.fastq.gz to 242M_2.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 242M_2.fastq.gz (86793768 sequences in total) Input files are 242M_1.fastq.gz_C_to_T.fastq and 242M_1.fastq.gz_G_to_A.fastq and 242M_2.fastq.gz_C_to_T.fastq and 242M_2.fastq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/scrubbed/sr320/github/project-mytilus-methylation/output/01-bismark-init/ with the specified options: -q --score-min L,0,-0.6 -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 242M_1.fastq.gz_C_to_T.fastq and 242M_2.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00469:254:22HGFVLT4:2:1101:1251:1014_1:N:0:ATCGACAT+TGCGTAAC/1 99 NC_086375.1_CT_converted 32589938 2 151M = 32590050 252 AAAAATAATGGTAATTTGAAGGTATAGATGTGTTTATGTGATATTATGATTGTGTTTATGGAATTATAATGTGTAATTTTTTTTTTTAGATAATATAAATTTATTTTTGATGATTTTTGTATATGGTATAATAATTATATTTTTGTTTTGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II9I9IIIIIIIIIIIIIIIIIIIIIII-II9III-IIIIIIIIII9I9IIIIIIIII AS:i:-36 XS:i:-48 XN:i:0 XM:i:6 XO:i:0 XG:i:0 NM:i:6 MD:Z:26T20A36A15A20G6A22 YS:i:-55 YT:Z:CP LH00469:254:22HGFVLT4:2:1101:1251:1014_2:N:0:ATCGACAT+TGCGTAAC/2 147 NC_086375.1_CT_converted 32590050 2 70M6I64M5I6M = 32589938 -252 ATTTTTGTAGATGGTAAAATAATTATATTTTTGTTTTGTTAGTTTTATTTAAAATTAAATGTTTAAAAAGTAATTATAATATATGATTTGTTTGTGGATTTTGTATTAGTGTGTTGTTGTAGTTATTTGTTTGATTATTATTTTTTTTTTT IIII9IIIIIIIIIIII9IIIII99IIIIIIII-IIIIIIIIII-IIII9IIIIIIIIIIII-III9IIIIII99II99III-II-IIIIIIIIIII9IIIII-9IIIIIII9I99IIIIIII-IIIIIIIIIIIIIIIIIIII9I-IIII AS:i:-55 XS:i:-52 XN:i:0 XM:i:2 XO:i:2 XG:i:11 NM:i:13 MD:Z:126A8A4 YS:i:-36 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 242M_1.fastq.gz_G_to_A.fastq and 242M_2.fastq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00469:254:22HGFVLT4:2:1101:1251:1014_1:N:0:ATCGACAT+TGCGTAAC/1 77 * 0 0 * * 0 0 AAAAATAATAATAATTTAAAAATATAAATATATTTATATAATATTATAATTATATTTATAAAATTATAATATATAATTTTTTTTTTTAAATAATATAAATCTATTTTTAATAATTTTTATATATAATACAATAATTATATTTTTATTTTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II9I9IIIIIIIIIIIIIIIIIIIIIII-II9III-IIIIIIIIII9I9IIIIIIIII YT:Z:UP LH00469:254:22HGFVLT4:2:1101:1251:1014_2:N:0:ATCGACAT+TGCGTAAC/2 141 * 0 0 * * 0 0 GGGAAGAGGAGTAATAATTAAATAAATAATTATAATAATATATTAATATAAAATTTATAAATAAATTATATATTATAATTATTTTTTAAATATTTAATTTTAAATAAAATTAATAAAATAAAAATATAATTATTTTATTATTTATAAAAAT IIII-I9IIIIIIIIIIIIIIIIIIII-IIIIIII99I9IIIIIII9-IIIII9IIIIIIIIIII-II-III99II99IIIIII9III-IIIIIIIIIIII9IIII-IIIIIIIIII-IIIIIIII99IIIII9IIIIIIIIIIII9IIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 242M_1.fastq.gz_G_to_A.fastq and 242M_2.fastq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00469:254:22HGFVLT4:2:1101:1251:1014_1:N:0:ATCGACAT+TGCGTAAC/1 77 * 0 0 * * 0 0 AAAAATAATAATAATTTAAAAATATAAATATATTTATATAATATTATAATTATATTTATAAAATTATAATATATAATTTTTTTTTTTAAATAATATAAATCTATTTTTAATAATTTTTATATATAATACAATAATTATATTTTTATTTTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II9I9IIIIIIIIIIIIIIIIIIIIIII-II9III-IIIIIIIIII9I9IIIIIIIII YT:Z:UP LH00469:254:22HGFVLT4:2:1101:1251:1014_2:N:0:ATCGACAT+TGCGTAAC/2 141 * 0 0 * * 0 0 GGGAAGAGGAGTAATAATTAAATAAATAATTATAATAATATATTAATATAAAATTTATAAATAAATTATATATTATAATTATTTTTTAAATATTTAATTTTAAATAAAATTAATAAAATAAAAATATAATTATTTTATTATTTATAAAAAT IIII-I9IIIIIIIIIIIIIIIIIIII-IIIIIII99I9IIIIIII9-IIIII9IIIIIIIIIII-II-III99II99IIIIII9III-IIIIIIIIIIII9IIII-IIIIIIIIII-IIIIIIII99IIIII9IIIIIIIIIIII9IIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 242M_1.fastq.gz_C_to_T.fastq and 242M_2.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00469:254:22HGFVLT4:2:1101:1251:1014_1:N:0:ATCGACAT+TGCGTAAC/1 83 NC_086384.1_GA_converted 22650336 0 107M4D44M = 22650234 -257 ACAAAACAAAAATATAATTATTATACCATATACAAAAATCATCAAAAATAAATTTATATTATCTAAAAAAAAAAATTACACATTATAATTCCATAAACACAATCATAATATCACATAAACACATCTATACCTTCAAATTACCATTATTTTT IIIIIIIII9I9IIIIIIIIII-III9II-IIIIIIIIIIIIIIIIIIIIIII9I9II9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-53 XS:i:-42 XN:i:0 XM:i:6 XO:i:1 XG:i:4 NM:i:10 MD:Z:22T6C20T15T32T7^AATT17A26 YS:i:-58 YT:Z:CP LH00469:254:22HGFVLT4:2:1101:1251:1014_2:N:0:ATCGACAT+TGCGTAAC/2 163 NC_086384.1_GA_converted 22650234 0 1M4I66M6I74M = 22650336 257 AAAAAAAAAAATAATAATCAAACAAATAACTACAACAACACACTAATACAAAATCCACAAACAAATCATATATTATAATTACTTTTTAAACATTTAATTTTAAATAAAACTAACAAAACAAAAATATAATTATTTTACCATCTACAAAAAT IIII-I9IIIIIIIIIIIIIIIIIIII-IIIIIII99I9IIIIIII9-IIIII9IIIIIIIIIII-II-III99II99IIIIII9III-IIIIIIIIIIII9IIII-IIIIIIIIII-IIIIIIII99IIIII9IIIIIIIIIIII9IIII AS:i:-58 XS:i:-58 XN:i:0 XM:i:3 XO:i:2 XG:i:10 NM:i:13 MD:Z:5T8T60A65 YS:i:-53 YT:Z:CP >>> Writing bisulfite mapping results to 242M_1_bismark_bt2_pe.bam <<< Reading in the sequence files ../data/raw-wgbs/242M_1.fastq.gz and ../data/raw-wgbs/242M_2.fastq.gz Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1101:48000:2765_1:N:0:ATCGCCAT+TGCGTAAC NW_026963361.1 3 Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1125:22016:17963_1:N:0:ATCGCCAT+TGCGTAAC NW_026963564.1 18986 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1136:36072:5847_1:N:0:ATCGCCAT+TGCGTAAC NW_026963784.1 3 Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1140:44593:12696_1:N:0:ATCGCCAT+TGCGTAAC NW_026963452.1 1 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1152:14522:22642_1:N:0:ATCGCCAT+TGCGTAAC NW_026963743.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1154:10168:26116_1:N:0:ATCGCCAT+TGCGTAAC NW_026963389.1 32276 Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1163:23909:28329_1:N:0:ATCGCAAT+TGCGTAAC NW_026963795.1 20629 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1168:49165:7612_1:N:0:ATCGCCAT+TGCGTAAC NW_026963581.1 3 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1171:11123:16226_1:N:0:ATCGCCAT+TGCGTAAC NW_026963775.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1171:11140:16226_1:N:0:ATCGCCAT+TGCGTAAC NW_026963775.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1171:11131:16240_1:N:0:ATCGCCAT+TGCGTAAC NW_026963775.1 1 Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1178:7490:18706_1:N:0:ATCGCCAT+TGCGTAAC NW_026963564.1 18984 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1181:50630:28105_1:N:0:ATCGCCAT+TGCGTAAC NW_026963550.1 42749 Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1196:6381:20821_1:N:0:ATCGCCAT+TGCGTAAC NW_026963809.1 20304 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1203:39673:11212_1:N:0:ATCGCCAT+TGCGTAAC NW_026963624.1 20273 Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1222:9602:3031_1:N:0:ATCGCCAT+TGCGTAAC NW_026963394.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1222:28416:28988_1:N:0:ATCGCCAT+TGCGTAAC NW_026963778.1 24088 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1227:22533:5076_1:N:0:ATCGCCAT+TGCGTAAC NW_026963422.1 18011 Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1233:50233:21059_1:N:0:ATCGCCAT+TGCGTAAC NW_026963566.1 1 Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1252:10201:11716_1:N:0:ATCGCCAT+TGCGTAAC NW_026963359.1 23004 Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1267:30836:27937_1:N:0:ATCGCCAT+TGCGTAAC NW_026963781.1 28263 Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1273:29501:20443_1:N:0:ATCGCCAT+TGCGTAAC NW_026963771.1 24010 Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1281:21231:17333_1:N:0:ATCGCCAT+TGCGTAAC NW_026963680.1 23006 Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1296:30844:24505_1:N:0:ATCGCCAT+TGCGTAAC NW_026963533.1 1 Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1333:4399:6407_1:N:0:ATCGCCAT+TGCGTAAC NW_026963430.1 2 Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1358:1923:15484_1:N:0:ATCGCCAT+TGCGTAAC NW_026963508.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1358:10816:20793_1:N:0:ATCGCCAT+TGCGTAAC NW_026963778.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1368:40474:6211_1:N:0:ATCGCCAT+TGCGTAAC NW_026963642.1 22022 Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1372:47725:23861_1:N:0:ATCGCCAT+TGCGTAAC NW_026963446.1 20331 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1373:9521:12136_1:N:0:ATCGCCAT+TGCGTAAC NW_026963443.1 56322 Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1381:51803:11170_1:N:0:ATCGCCAT+TGCGTAAC NW_026963616.1 1 Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1397:29104:3956_1:N:0:ATCGCCAT+TGCGTAAC NW_026963510.1 2 Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1419:6211:29044_1:N:0:ATCGCCAT+TGCGTAAC NW_026963471.1 1 Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1448:45556:7976_1:N:0:ATCGCCAT+TGCGTAAC NW_026963564.1 18984 Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1485:1146:19322_1:N:0:ATCGCAAT+TGCGTAAC NW_026963642.1 22022 Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2104:49270:19644_1:N:0:ATCGCCAT+TGCGTAAC NW_026963564.1 18984 Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2112:49780:12711_1:N:0:ATCGCCAT+TGCGTAAC NW_026963360.1 21736 Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2128:3800:3269_1:N:0:ATCGCCAT+TGCGTAAC NW_026963430.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2129:11107:7570_1:N:0:ATCGCCAT+TGCGTAAC NW_026963781.1 28259 Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2148:8437:11940_1:N:0:ATCGCCAT+TGCGTAAC NW_026963443.1 56317 Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2170:7838:6953_1:N:0:ATCGCCAT+TGCGTAAC NW_026963454.1 23500 Processed 38000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2175:17427:16437_1:N:0:ATCGCCAT+TGCGTAAC NW_026963579.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2175:46923:25976_1:N:0:ATCGCCAT+TGCGTAAC NW_026963333.1 249855 Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2206:21206:1238_1:N:0:ATCGCCCT+TGCGTAAC NW_026963700.1 2 Processed 41000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2217:37690:4810_1:N:0:ATCGCCAT+TGCGTAAC NW_026963553.1 3 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2217:37698:4824_1:N:0:ATCGCCAT+TGCGTAAC NW_026963553.1 3 Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2227:8882:28819_1:N:0:ATCGCCAT+TGCGTAAC NW_026963743.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2231:31524:15568_1:N:0:ATCGCCAT+TGCGTAAC NW_026963778.1 1 Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2253:4577:17081_1:N:0:ATCGCCAT+TGCGTAAC NW_026963677.1 25094 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2255:32972:20989_1:N:0:ATCGCCAT+TGCGTAAC NW_026963443.1 56317 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2257:20300:24575_1:N:0:ATCGCCAT+TGCGTAAC NW_026963415.1 2 Processed 45000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2267:16893:12318_1:N:0:ATCGCCAT+TGCGTAAC NW_026963781.1 28268 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2276:16092:22054_1:N:0:ATCGCCAT+TGCGTAAC NW_026963415.1 3 Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2294:21846:8396_1:N:0:ATCGCCAT+TGCGTAAC NW_026963554.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2294:32018:27433_1:N:0:ATCGCCAT+TGCGTAAC NW_026963443.1 56316 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2297:25722:6057_1:N:0:ATCGCCAT+TGCGTAAC NW_026963550.1 42749 Processed 48000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2307:8210:23819_1:N:0:ATCGCCAT+TGCGTAAC NW_026963564.1 18995 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2314:3881:2625_1:N:0:ATCGCCAT+TGCGTAAC NW_026963781.1 28267 Processed 49000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2319:20324:18734_1:N:0:ATCGCCAT+TGCGTAAC NW_026963734.1 3 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2328:23165:22082_1:N:0:ATCGCCAT+TGCGTAAC NW_026963781.1 28268 Processed 50000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2336:43347:20289_1:N:0:ATCGCCAT+TGCGTAAC NW_026963697.1 1 Processed 51000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2355:34283:21858_1:N:0:ATCGCCAT+TGCGTAAC NW_026963501.1 19408 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2355:34283:21886_1:N:0:ATCGCCAT+TGCGTAAC NW_026963501.1 19408 Processed 52000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2368:33199:21998_1:N:0:ATCGCCAT+TGCGTAAC NW_026963501.1 19422 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2370:2262:15568_1:N:0:ATCGCCAT+TGCGTAAC NW_026963303.1 1 Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2387:32778:2891_1:N:0:ATCGCCAT+TGCGTAAC NW_026963415.1 3 Processed 55000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2406:49149:3325_1:N:0:ATCGCCAT+TGCGTAAC NW_026963710.1 3 Processed 56000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2421:30245:10805_1:N:0:ATCGCCAT+TGCGTAAC NW_026963781.1 28259 Processed 57000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2441:38839:17417_1:N:0:ATCGCCAT+TGCGTAAC NW_026963402.1 95196 Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2455:22517:28301_1:N:0:ATCGCCAT+TGCGTAAC NW_026963415.1 3 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2457:13106:5987_1:N:0:ATCGCCAT+TGCGTAAC NW_026963411.1 26095 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2468:29137:27937_1:N:0:ATCGCCAT+TGCGTAAC NW_026963430.1 1 Processed 60000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2478:28214:27825_1:N:0:ATCGCCAT+TGCGTAAC NW_026963477.1 2 Processed 61000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2495:37512:2485_1:N:0:ATCGCCAT+TGCGTAAC NW_026963501.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2495:37520:2499_1:N:0:ATCGCCAT+TGCGTAAC NW_026963501.1 1 Processed 62000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1116:1550:15288_1:N:0:ATCGCCAT+TGCGTAAC NW_026963737.1 15325 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1124:24670:11800_1:N:0:ATCGCAAT+TGCGTAAC NW_026963734.1 2 Processed 63000000 sequence pairs so far Processed 64000000 sequence pairs so far Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1251:45912:8620_1:N:0:ATCGCCAT+TGCGTAAC NW_026963800.1 22234 Processed 67000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1269:8680:26228_1:N:0:ATCGCCAT+TGCGTAAC NW_026963677.1 25096 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1277:13114:6421_1:N:0:ATCGCCAT+TGCGTAAC NW_026963743.1 1 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1281:32608:9433_1:N:0:ATCGCCAT+TGCGTAAC NW_026963307.1 124869 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1282:42432:3577_1:N:0:ATCGCCAT+TGCGTAAC NW_026963778.1 1 Processed 68000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1302:10330:4152_1:N:0:ATCGCCAT+TGCGTAAC NW_026963389.1 32281 Processed 69000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1317:17589:13299_1:N:0:ATCGCCAT+TGCGTAAC NW_026963743.1 1 Processed 70000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1358:30100:16773_1:N:0:ATCGCCAT+TGCGTAAC NW_026963677.1 25091 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1361:21279:21143_1:N:0:ATCGCCAT+TGCGTAAC NW_026963781.1 28258 Processed 71000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1382:36784:17781_1:N:0:ATCGCCAT+TGCGTAAC NC_086377.1 88128905 Processed 72000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1431:29315:24519_1:N:0:ATCGCCAT+TGCGTAAC NC_086385.1 3 Processed 73000000 sequence pairs so far Processed 74000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1492:22558:1532_1:N:0:ATCGCCAT+TGCGTAAC NW_026963771.1 24021 Processed 75000000 sequence pairs so far Processed 76000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2148:2991:6183_1:N:0:ATCGCCAT+TGCGTAAC NW_026963704.1 2 Processed 77000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2188:35020:26802_1:N:0:ATCGCCAT+TGCGTAAC NW_026963677.1 25094 Processed 78000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2221:13438:6337_1:N:0:ATCGCCAT+TGCGTAAC NW_026963404.1 2 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2231:34065:9741_1:N:0:ATCGCCAT+TGCGTAAC NW_026963614.1 2 Processed 79000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2266:40628:27349_1:N:0:ATCGCCAT+TGCGTAAC NW_026963308.1 1 Processed 80000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2278:23650:2023_1:N:0:ATCGCCAT+TGCGTAAC NW_026963728.1 26562 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2285:46745:16927_1:N:0:ATCGCCAT+TGCGTAAC NW_026963317.1 4467280 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2308:8218:14756_1:N:0:ATCGCCAT+TGCGTAAC NW_026963316.1 1 Processed 81000000 sequence pairs so far Processed 82000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2351:26353:10679_1:N:0:ATCGCCAT+TGCGTAAC NW_026963743.1 1 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2359:20753:14574_1:N:0:ATCGCCAT+TGCGTAAC NW_026963771.1 24008 Processed 83000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2405:42303:20555_1:N:0:ATCGCCAT+TGCGTAAC NW_026963326.1 2 Processed 84000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2433:14320:12963_1:N:0:ATCGCCAT+TGCGTAAC NW_026963550.1 42749 Processed 85000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2455:41097:12556_1:N:0:ATCGCCAT+TGCGTAAC NW_026963589.1 26167 Processed 86000000 sequence pairs so far 86793768 reads; of these: 86793768 (100.00%) were paired; of these: 86712004 (99.91%) aligned concordantly 0 times 14442 (0.02%) aligned concordantly exactly 1 time 67322 (0.08%) aligned concordantly >1 times 0.09% overall alignment rate 86793768 reads; of these: 86793768 (100.00%) were paired; of these: 86716464 (99.91%) aligned concordantly 0 times 13240 (0.02%) aligned concordantly exactly 1 time 64064 (0.07%) aligned concordantly >1 times 0.09% overall alignment rate 86793768 reads; of these: 86793768 (100.00%) were paired; of these: 45434516 (52.35%) aligned concordantly 0 times 13572332 (15.64%) aligned concordantly exactly 1 time 27786920 (32.01%) aligned concordantly >1 times 47.65% overall alignment rate 86793768 reads; of these: 86793768 (100.00%) were paired; of these: 45407587 (52.32%) aligned concordantly 0 times 13585069 (15.65%) aligned concordantly exactly 1 time 27801112 (32.03%) aligned concordantly >1 times 47.68% overall alignment rate Processed 86793768 sequences in total Successfully deleted the temporary files 242M_1.fastq.gz_C_to_T.fastq, 242M_1.fastq.gz_G_to_A.fastq, 242M_2.fastq.gz_C_to_T.fastq and 242M_2.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 86793768 Final Cytosine Methylation Report ================================= Total number of C's analysed: 2099732888 Total methylated C's in CpG context: 39803056 Total methylated C's in CHG context: 10013472 Total methylated C's in CHH context: 48291258 Total methylated C's in Unknown context: 2784447 Total unmethylated C's in CpG context: 240672757 Total unmethylated C's in CHG context: 345973129 Total unmethylated C's in CHH context: 1414979216 Total unmethylated C's in Unknown context: 9128068 C methylated in CpG context: 14.2% C methylated in CHG context: 2.8% C methylated in CHH context: 3.3% C methylated in Unknown context (CN or CHN): 23.4% Bismark completed in 0d 5h 40m 1s ==================== Bismark run complete ====================