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/239M_1.fastq.gz ../data/raw-wgbs/239M_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/239M_1.fastq.gz and ../data/raw-wgbs/239M_2.fastq.gz Input files are in FastQ format Writing a C -> T converted version of the input file 239M_1.fastq.gz to 239M_1.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 239M_1.fastq.gz to 239M_1.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 239M_1.fastq.gz (108112211 sequences in total) Writing a C -> T converted version of the input file 239M_2.fastq.gz to 239M_2.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 239M_2.fastq.gz to 239M_2.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 239M_2.fastq.gz (108112211 sequences in total) Input files are 239M_1.fastq.gz_C_to_T.fastq and 239M_1.fastq.gz_G_to_A.fastq and 239M_2.fastq.gz_C_to_T.fastq and 239M_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 239M_1.fastq.gz_C_to_T.fastq and 239M_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: LH00469:254:22HGFVLT4:2:1101:2206:1014_1:N:0:GAGCAGTA+TGAGCTGT/1 77 * 0 0 * * 0 0 TTTGGAATGTGTTAATGTTAGAATAAATGAATATTAAATATTATTGATTTATTATTATTAGTTTTTTATAAATTAATTTAATTATAAATTTATATATTGTTGATGATTTTAAATAGGAGGGAGGGTAGGAGGGGTTTTGATTTTGAAATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIII9IIIIIIIII9IIIIIIII9II9IIIIII9IIII-I-IIIII9I YT:Z:UP LH00469:254:22HGFVLT4:2:1101:2206:1014_2:N:0:GAGCAGTA+TGAGCTGT/2 141 * 0 0 * * 0 0 AAAAATTCAATAATTATTTAATACTATATATCATTTTTTAAAATTTATTATTTTTATCACCTTAACAAAATAAAAAAACAAAACCTAAATATACTATTTAAAAAAAAATAAAACCTTAATCAAAACTCCAAAATCTAATATTTTTAATTTC I9IIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-9IIIIIIIIIIIIIIIIIIIII-IIIIIIIIII9IIIIIIIIII-IIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 239M_1.fastq.gz_G_to_A.fastq and 239M_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: LH00469:254:22HGFVLT4:2:1101:2206:1014_1:N:0:GAGCAGTA+TGAGCTGT/1 77 * 0 0 * * 0 0 TTTAAAATATATTAATATTAAAATAAATAAATATTAAATATTATTAATTTATTATTATTAATTTTTTATAAATTAATTTAATTATAAATTTATATATTATTAATAATTTTAAATAAAAAAAAAAATAAAAAAAATTTTAATTTCAAAATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIII9IIIIIIIII9IIIIIIII9II9IIIIII9IIII-I-IIIII9I YT:Z:UP LH00469:254:22HGFVLT4:2:1101:2206:1014_2:N:0:GAGCAGTA+TGAGCTGT/2 141 * 0 0 * * 0 0 GGAGGTTTAATAATTATTTAATATTATATATTATTTTTTAAAATTTATTATTTTTATTGTTTTAATAAAATAAAAAAATAAAATTTAAATATATTATTTAAAAAAAAATAAAATTTTAATTGAAATTTTGAAATTTAATATTTTTAATTTT I9IIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-9IIIIIIIIIIIIIIIIIIIII-IIIIIIIIII9IIIIIIIIII-IIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 239M_1.fastq.gz_G_to_A.fastq and 239M_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: LH00469:254:22HGFVLT4:2:1101:2206:1014_1:N:0:GAGCAGTA+TGAGCTGT/1 77 * 0 0 * * 0 0 TTTAAAATATATTAATATTAAAATAAATAAATATTAAATATTATTAATTTATTATTATTAATTTTTTATAAATTAATTTAATTATAAATTTATATATTATTAATAATTTTAAATAAAAAAAAAAATAAAAAAAATTTTAATTTCAAAATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIII9IIIIIIIII9IIIIIIII9II9IIIIII9IIII-I-IIIII9I YT:Z:UP LH00469:254:22HGFVLT4:2:1101:2206:1014_2:N:0:GAGCAGTA+TGAGCTGT/2 141 * 0 0 * * 0 0 GGAGGTTTAATAATTATTTAATATTATATATTATTTTTTAAAATTTATTATTTTTATTGTTTTAATAAAATAAAAAAATAAAATTTAAATATATTATTTAAAAAAAAATAAAATTTTAATTGAAATTTTGAAATTTAATATTTTTAATTTT I9IIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-9IIIIIIIIIIIIIIIIIIIII-IIIIIIIIII9IIIIIIIIII-IIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 239M_1.fastq.gz_C_to_T.fastq and 239M_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: LH00469:254:22HGFVLT4:2:1101:2206:1014_1:N:0:GAGCAGTA+TGAGCTGT/1 77 * 0 0 * * 0 0 TTTGGAATGTGTTAATGTTAGAATAAATGAATATTAAATATTATTGATTTATTATTATTAGTTTTTTATAAATTAATTTAATTATAAATTTATATATTGTTGATGATTTTAAATAGGAGGGAGGGTAGGAGGGGTTTTGATTTTGAAATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIII9IIIIIIIII9IIIIIIII9II9IIIIII9IIII-I-IIIII9I YT:Z:UP LH00469:254:22HGFVLT4:2:1101:2206:1014_2:N:0:GAGCAGTA+TGAGCTGT/2 141 * 0 0 * * 0 0 AAAAATTCAATAATTATTTAATACTATATATCATTTTTTAAAATTTATTATTTTTATCACCTTAACAAAATAAAAAAACAAAACCTAAATATACTATTTAAAAAAAAATAAAACCTTAATCAAAACTCCAAAATCTAATATTTTTAATTTC I9IIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-9IIIIIIIIIIIIIIIIIIIII-IIIIIIIIII9IIIIIIIIII-IIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIII YT:Z:UP >>> Writing bisulfite mapping results to 239M_1_bismark_bt2_pe.bam <<< Reading in the sequence files ../data/raw-wgbs/239M_1.fastq.gz and ../data/raw-wgbs/239M_2.fastq.gz Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1118:43468:6715_1:N:0:GAGCAGTA+TGAGCTGT NW_026963696.1 1 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1126:48906:16381_1:N:0:GAGCAGTA+TGAGCTGT NW_026963443.1 56316 Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1156:11674:8438_1:N:0:GAGCAGTA+TGAGCTGT NW_026963415.1 1 Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1179:1720:2443_1:N:0:GAGCAGTA+TAAGCTGT NW_026963443.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1183:6074:11408_1:N:0:GAGCAGTA+TGAGCTGT NW_026963443.1 1 Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1206:21028:2947_1:N:0:GAGCAGTA+TGAGCTGT NW_026963725.1 2 Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1217:4253:6575_1:N:0:GAGCAGTA+TGAGCTGT NW_026963725.1 1 Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1224:42715:24771_1:N:0:GAGCAGTA+TGAGCTGT NW_026963415.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1224:42707:24785_1:N:0:GAGCAGTA+TGAGCTGT NW_026963415.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1226:47652:18580_1:N:0:GAGCAGTA+TGAGCTGT NW_026963379.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1228:3355:10651_1:N:0:GAGCAGTA+TGAGCTGT NW_026963341.1 2 Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1231:39187:22446_1:N:0:GAGCAGTA+TGAGCTGT NW_026963307.1 124868 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1233:13009:29408_1:N:0:GAGCAGTA+TGAGCTGT NW_026963319.1 1 Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1246:22194:26452_1:N:0:GAGCAGTA+TGAGCTGT NW_026963814.1 8571 Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1261:12151:6435_1:N:0:GAGCAGTA+TGAGCTGT NW_026963443.1 2 Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1268:48259:17977_1:N:0:GAGCAGTA+TGAGCTGT NW_026963611.1 1 Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1277:45807:8018_1:N:0:GAGCAGTA+TGAGCTGT NW_026963443.1 56340 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1279:24710:17305_1:N:0:GAGCAGTA+TGAGCTGT NW_026963595.1 3 Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1321:26539:22180_1:N:0:GAGCAGTA+TGAGCTGT NW_026963684.1 18459 Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1336:3363:24869_1:N:0:GAGCAGTA+TGAGCTGT NW_026963307.1 124865 Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1345:46163:21325_1:N:0:GAGCAGTA+TGAGCTGT NW_026963335.1 1 Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1444:31079:21437_1:N:0:GAGCAGTA+TGAGCTGT NW_026963677.1 25093 Processed 39000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1448:9424:9811_1:N:0:GAGCAGTA+TGAGCTGT NW_026963377.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1450:15153:19784_1:N:0:GAGCAGTA+TGAGCTGT NW_026963443.1 56335 Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1461:49246:7948_1:N:0:GAGCAGTA+TGAGCTGT NW_026963609.1 1 Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1481:29533:6911_1:N:0:GAGCAGTA+TGAGCTGT NW_026963564.1 18986 Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2128:19742:2233_1:N:0:GAGCAGTA+TGAGCTGT NW_026963443.1 56330 Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2156:18471:11548_1:N:0:GAGCAGTA+TGAGCTGT NW_026963303.1 1 Processed 51000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2163:36768:18678_1:N:0:GAGCAGTA+TGAGCTGT NW_026963299.1 2 Processed 52000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2171:15890:29184_1:N:0:GAGCAGTA+TGAGCTGT NW_026963319.1 1 Processed 53000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2177:25228:13803_1:N:0:GAGCAGTA+TGAGCTGT NW_026963712.1 1 Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2207:7158:28497_1:N:0:GAGCAGTA+TGAGCTGT NW_026963564.1 18991 Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2268:51042:27026_1:N:0:GAGCAGTA+TGAGCTGT NW_026963443.1 56332 Processed 63000000 sequence pairs so far Processed 64000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2290:11156:12080_1:N:0:GAGCAGTA+TGAGCTGT NW_026963369.1 120934 Processed 65000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2294:14061:18426_1:N:0:GAGCAGTA+TGAGCTGT NW_026963341.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2294:14053:18440_1:N:0:GAGCAGTA+TGAGCTGT NW_026963341.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2302:5426:11044_1:N:0:GAGCAGTA+TGAGCTGT NW_026963443.1 1 Processed 66000000 sequence pairs so far Processed 67000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2320:36582:27181_1:N:0:GAGCAGTA+TGAGCTGT NW_026963461.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2320:36590:27195_1:N:0:GAGCAGTA+TGAGCTGT NW_026963461.1 1 Processed 68000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2322:19110:2625_1:N:0:GAGCAGTA+TGAGCTGT NW_026963415.1 1 Processed 69000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2331:9553:28329_1:N:0:GAGCAGTA+TGAGCTGT NW_026963675.1 20000 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2331:9529:28343_1:N:0:GAGCAGTA+TGAGCTGT NW_026963675.1 20000 Processed 70000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2349:34372:5258_1:N:0:GAGCAGTA+TGAGCTGT NW_026963443.1 56330 Processed 71000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2354:32600:1210_1:N:0:GAGCAGTA+TGAGCTGT NW_026963771.1 24013 Processed 72000000 sequence pairs so far Processed 73000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2370:42635:9503_1:N:0:GAGCAGTA+TGAGCTGT NW_026963443.1 56325 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2373:23148:12584_1:N:0:GAGCAGTA+TGAGCTGT NW_026963415.1 1 Processed 74000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2383:4148:27293_1:N:0:GAGCAGTA+TGAGCTGT NW_026963443.1 56315 Processed 75000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2392:35109:17655_1:N:0:GAGCAGTA+TGAGCTGT NW_026963443.1 56322 Processed 76000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2412:20486:25430_1:N:0:GAGCAGTA+TGAGCTGT NW_026963341.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2412:20494:25444_1:N:0:GAGCAGTA+TGAGCTGT NW_026963341.1 1 Processed 77000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2423:3395:10525_1:N:0:GAGCAGTA+TGAGCTGT NW_026963677.1 25086 Processed 78000000 sequence pairs so far Processed 79000000 sequence pairs so far Processed 80000000 sequence pairs so far Processed 81000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2460:3719:8536_1:N:0:GAGCAGTA+TGAGCTTT NW_026963307.1 124868 Processed 82000000 sequence pairs so far Processed 83000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2475:37407:12192_1:N:0:GAGCAGTA+TGAGCTGT NW_026963404.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2477:44415:5440_1:N:0:GAGCAGTA+TGAGCTGT NW_026963415.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2478:24128:7696_1:N:0:GAGCAGTA+TGAGCTGT NW_026963687.1 1 Processed 84000000 sequence pairs so far Processed 85000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1102:29946:14686_1:N:0:GAGCAGTA+TGAGCTGT NW_026963443.1 1 Processed 86000000 sequence pairs so far Processed 87000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1164:6438:6351_1:N:0:GAGCAGTA+TGAGCTGT NW_026963341.1 1 Processed 88000000 sequence pairs so far Processed 89000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1220:27737:17221_1:N:0:GAGCAGTA+TGAGCTGT NW_026963611.1 19981 Processed 90000000 sequence pairs so far Processed 91000000 sequence pairs so far Processed 92000000 sequence pairs so far Processed 93000000 sequence pairs so far Processed 94000000 sequence pairs so far Processed 95000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1426:37188:7304_1:N:0:GAGCAGTA+TGAGCTGT NW_026963564.1 18985 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1437:28497:11478_1:N:0:GAGCAGTA+TGAGCTGT NW_026963772.1 22149 Processed 96000000 sequence pairs so far Processed 97000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2107:33733:4376_1:N:0:GAGCAGTA+TGAGCTGT NW_026963650.1 2 Processed 98000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2162:2910:7247_1:N:0:GAGCAGTA+TGAGCTGT NW_026963718.1 1 Processed 99000000 sequence pairs so far Processed 100000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2203:2554:20303_1:N:0:GAGCAGTA+TGAGCTGT NW_026963588.1 48211 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2204:23950:25878_1:N:0:GAGCAGTA+TGAGCTGT NW_026963303.1 1 Processed 101000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2252:5580:3802_1:N:0:GAGCAGTA+TGAGCTGT NW_026963564.1 18986 Processed 102000000 sequence pairs so far Processed 103000000 sequence pairs so far Processed 104000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2377:21983:18412_1:N:0:GAGCAGTA+TGAGCTGT NW_026963725.1 1 Processed 105000000 sequence pairs so far Processed 106000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2430:25835:22782_1:N:0:GAGCAGTA+TGAGCTGT NW_026963677.1 25091 Processed 107000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2473:2359:12066_1:N:0:GAGCAGTA+TGAGCTGT NW_026963684.1 18449 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2476:25511:11436_1:N:0:GAGCAGTA+TGAGCTGT NW_026963341.1 2 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2476:25657:13901_1:N:0:GAGCAGTA+TGAGCTGT NW_026963564.1 18997 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2479:2942:13159_1:N:0:GAGCAGTA+TGAGCTGT NW_026963443.1 56334 Processed 108000000 sequence pairs so far 108112211 reads; of these: 108112211 (100.00%) were paired; of these: 63599944 (58.83%) aligned concordantly 0 times 18701991 (17.30%) aligned concordantly exactly 1 time 25810276 (23.87%) aligned concordantly >1 times 41.17% overall alignment rate 108112211 reads; of these: 108112211 (100.00%) were paired; of these: 108036660 (99.93%) aligned concordantly 0 times 26931 (0.02%) aligned concordantly exactly 1 time 48620 (0.04%) aligned concordantly >1 times 0.07% overall alignment rate 108112211 reads; of these: 108112211 (100.00%) were paired; of these: 63597867 (58.83%) aligned concordantly 0 times 18714158 (17.31%) aligned concordantly exactly 1 time 25800186 (23.86%) aligned concordantly >1 times 41.17% overall alignment rate 108112211 reads; of these: 108112211 (100.00%) were paired; of these: 108039991 (99.93%) aligned concordantly 0 times 26095 (0.02%) aligned concordantly exactly 1 time 46125 (0.04%) aligned concordantly >1 times 0.07% overall alignment rate Processed 108112211 sequences in total Could not delete temporary files properly: No such file or directory Final Alignment report ====================== Sequence pairs analysed in total: 108112211 Final Cytosine Methylation Report ================================= Total number of C's analysed: 2378079434 Total methylated C's in CpG context: 39483148 Total methylated C's in CHG context: 11296787 Total methylated C's in CHH context: 55941539 Total methylated C's in Unknown context: 3115796 Total unmethylated C's in CpG context: 232242348 Total unmethylated C's in CHG context: 368776059 Total unmethylated C's in CHH context: 1670339553 Total unmethylated C's in Unknown context: 10902559 C methylated in CpG context: 14.5% C methylated in CHG context: 3.0% C methylated in CHH context: 3.2% C methylated in Unknown context (CN or CHN): 22.2% Bismark completed in 0d 6h 15m 44s ==================== Bismark run complete ====================