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/241M_1.fastq.gz ../data/raw-wgbs/241M_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/241M_1.fastq.gz and ../data/raw-wgbs/241M_2.fastq.gz Input files are in FastQ format Writing a C -> T converted version of the input file 241M_1.fastq.gz to 241M_1.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 241M_1.fastq.gz to 241M_1.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 241M_1.fastq.gz (87063380 sequences in total) Writing a C -> T converted version of the input file 241M_2.fastq.gz to 241M_2.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 241M_2.fastq.gz to 241M_2.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 241M_2.fastq.gz (87063380 sequences in total) Input files are 241M_1.fastq.gz_C_to_T.fastq and 241M_1.fastq.gz_G_to_A.fastq and 241M_2.fastq.gz_C_to_T.fastq and 241M_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 241M_1.fastq.gz_C_to_T.fastq and 241M_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: LH00469:254:22HGFVLT4:2:1101:3581:1014_1:N:0:TTGCGAAG+AACACGCT/1 99 NC_086385.1_CT_converted 15645270 42 151M = 15645303 184 AAATGTTTTTTGAATTTAAAAATTTGTTGTTAATTAAGAAATTAAGTATTATGAATATGTTATTTTTAGAGAATTTTTTGATTAAATAAGAATGTATTTTTATAAGTTATGAATAAAATTTTTTTTAAAAATAGATGTAGTTTGTTATGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:29A121 YS:i:-18 YT:Z:CP LH00469:254:22HGFVLT4:2:1101:3581:1014_2:N:0:TTGCGAAG+AACACGCT/2 147 NC_086385.1_CT_converted 15645303 42 151M = 15645270 -184 TTAAGAAATTAAGTATTATGAATATGTTATTTTTAGAGAATTTTTTGATTAAATAAGAATGTATTTTTATAAGTTATGAATAAAATTTTTTTTAAAAATAGATGTAGTTTGTTATGAGATATGGGTTTTGATTAGTGTTGGAGTTTTTTTT IIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII9III9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIII9IIII9IIIIIIIII-9IIIII9IIIIIIIIIIIIIIIIIIII AS:i:-18 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:143G2G3G0 YS:i:-6 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 241M_1.fastq.gz_G_to_A.fastq and 241M_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: LH00469:254:22HGFVLT4:2:1101:3581:1014_1:N:0:TTGCGAAG+AACACGCT/1 77 * 0 0 * * 0 0 AAATATTTTTTAAATTTAAAAATTTATTATTAATTAAAAAATTAAATATTATAAATATATTATTTTTAAAAAATTTTTTAATTAAATAAAAATATATTTTTATAAATTATAAATAAAATTTTTTTTAAAAATAAATATAATTTATTATAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00469:254:22HGFVLT4:2:1101:3581:1014_2:N:0:TTGCGAAG+AACACGCT/2 141 * 0 0 * * 0 0 GAGGGAAATTTTAATATTAATTAAAATTTATATTTTATAATAAATTATATTTATTTTTAAAAAAAATTTTATTTATAATTTATAAAAATATATTTTTATTTAATTAAAAAATTTTTTAAAAATAATATATTTATAATATTTAATTTTTTAA IIIIIIIIIIIIIIIIIIII9IIIII9-IIIIIIIII9IIII9IIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III9IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 241M_1.fastq.gz_G_to_A.fastq and 241M_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: LH00469:254:22HGFVLT4:2:1101:3581:1014_1:N:0:TTGCGAAG+AACACGCT/1 77 * 0 0 * * 0 0 AAATATTTTTTAAATTTAAAAATTTATTATTAATTAAAAAATTAAATATTATAAATATATTATTTTTAAAAAATTTTTTAATTAAATAAAAATATATTTTTATAAATTATAAATAAAATTTTTTTTAAAAATAAATATAATTTATTATAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00469:254:22HGFVLT4:2:1101:3581:1014_2:N:0:TTGCGAAG+AACACGCT/2 141 * 0 0 * * 0 0 GAGGGAAATTTTAATATTAATTAAAATTTATATTTTATAATAAATTATATTTATTTTTAAAAAAAATTTTATTTATAATTTATAAAAATATATTTTTATTTAATTAAAAAATTTTTTAAAAATAATATATTTATAATATTTAATTTTTTAA IIIIIIIIIIIIIIIIIIII9IIIII9-IIIIIIIII9IIII9IIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III9IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 241M_1.fastq.gz_C_to_T.fastq and 241M_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: LH00469:254:22HGFVLT4:2:1101:3581:1014_1:N:0:TTGCGAAG+AACACGCT/1 77 * 0 0 * * 0 0 AAATGTTTTTTGAATTTAAAAATTTGTTGTTAATTAAGAAATTAAGTATTATGAATATGTTATTTTTAGAGAATTTTTTGATTAAATAAGAATGTATTTTTATAAGTTATGAATAAAATTTTTTTTAAAAATAGATGTAGTTTGTTATGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00469:254:22HGFVLT4:2:1101:3581:1014_2:N:0:TTGCGAAG+AACACGCT/2 141 * 0 0 * * 0 0 AAAAAAAACTCCAACACTAATCAAAACCCATATCTCATAACAAACTACATCTATTTTTAAAAAAAATTTTATTCATAACTTATAAAAATACATTCTTATTTAATCAAAAAATTCTCTAAAAATAACATATTCATAATACTTAATTTCTTAA IIIIIIIIIIIIIIIIIIII9IIIII9-IIIIIIIII9IIII9IIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III9IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIII YT:Z:UP >>> Writing bisulfite mapping results to 241M_1_bismark_bt2_pe.bam <<< Reading in the sequence files ../data/raw-wgbs/241M_1.fastq.gz and ../data/raw-wgbs/241M_2.fastq.gz Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1107:38046:13887_1:N:0:TTGCGAAG+AACACGCT NW_026963443.1 1 Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1130:13057:18706_1:N:0:TTGCGAAG+AACACGCT NW_026963736.1 25891 Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1143:40895:12795_1:N:0:TTGCGAAG+AACACGCT NW_026963372.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1145:43403:2009_1:N:0:TTGCGGAG+AACACGCT NW_026963809.1 1 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1146:45273:27461_1:N:0:TTGCGAAG+AACACGCT NW_026963377.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1155:17435:23651_1:N:0:TTGCGAAG+AACACGCT NW_026963422.1 18028 Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1156:8591:28679_1:N:0:TTGCGAAG+AACACGCT NW_026963743.1 1 Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1168:37447:5426_1:N:0:TTGCGAAG+AACACGCT NW_026963611.1 19974 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1168:9545:28875_1:N:0:TTGCGAAG+AACACGCT NW_026963598.1 29307 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1170:8113:14097_1:N:0:TTGCGAAG+AACACGCT NW_026963781.1 28256 Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1190:35861:9545_1:N:0:TTGCGAAG+AACACGCT NW_026963631.1 26232 Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1225:9699:25444_1:N:0:TTGCGAAG+AACACGCT NW_026963673.1 26131 Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1232:33854:4614_1:N:0:TTGCGAAG+AACACGCT NW_026963322.1 898851 Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1277:24095:23020_1:N:0:TTGCGAAG+AACACGCT NW_026963684.1 18447 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 LH00469:254:22HGFVLT4:2:1312:12879:12066_1:N:0:TTGCGAAG+AACACGCT NW_026963631.1 26227 Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1321:6244:5763_1:N:0:TTGCGAAG+AACACGCT NW_026963741.1 1 Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1381:14368:28847_1:N:0:TTGCGAAG+AACACGCT NW_026963771.1 24007 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1387:19232:7570_1:N:0:TTGCGAAG+AACACGCT NW_026963728.1 26553 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1389:45159:26536_1:N:0:TTGCGAAG+AACACGCT NW_026963677.1 25091 Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1396:16278:2653_1:N:0:TTGCGAAG+AACACGCT NW_026963443.1 56324 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1401:1227:8032_1:N:0:TTGCGAAG+AACACGCT NW_026963299.1 2 Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1412:5103:7878_1:N:0:TTGCGAAG+AACACGCT NW_026963348.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1412:5111:7892_1:N:0:TTGCGAAG+AACACGCT NW_026963348.1 1 Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1416:13252:4782_1:N:0:TTGCGAAG+AACACGCT NW_026963418.1 1 Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1444:7004:13803_1:N:0:TTGCGAAG+AACACGCT NW_026963707.1 3 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1445:40765:14447_1:N:0:TTGCGAAG+AACACGCT NW_026963734.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1445:2732:14616_1:N:0:TTGCGAAG+AACACGCT NW_026963443.1 56325 Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1458:43428:10511_1:N:0:TTGCGAAG+AACACGCT NW_026963422.1 18038 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1460:40959:23917_1:N:0:TTGCGAAG+AACACGCT NW_026963728.1 26562 Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1468:16472:18005_1:N:0:TTGCGAAG+AACACGCT NW_026963657.1 17829 Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1476:25406:16689_1:N:0:TTGCGAAG+AACACGCT NW_026963443.1 56321 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1483:37358:7542_1:N:0:TTGCGAAG+AACACGCT NW_026963771.1 24006 Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1496:14935:6295_1:N:0:TTGCGAAG+AACACGCT NW_026963307.1 124870 Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2113:8623:20583_1:N:0:TTGCGAAG+AACACGCT NW_026963478.1 20755 Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2131:14660:6715_1:N:0:TTGCGAAG+AACACGCT NW_026963608.1 21993 Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2162:28336:8508_1:N:0:TTGCGAAG+AACACGCT NW_026963422.1 18035 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2164:20842:12570_1:N:0:TTGCGAAG+AACACGCT NW_026963657.1 17827 Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2170:46495:29240_1:N:0:TTGCGAAG+AACACGCT NW_026963734.1 1 Processed 41000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2188:34041:22782_1:N:0:TTGCGAAG+AACACGCT NW_026963684.1 18449 Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2214:9359:7990_1:N:0:TTGCGAAG+AACACGCT NW_026963303.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2218:36751:15848_1:N:0:TTGCGAAG+AACACGCT NW_026963585.1 2 Processed 44000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2225:35610:18916_1:N:0:TTGCGAAG+AACACGCT NW_026963781.1 28257 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2229:35570:13019_1:N:0:TTGCGAAG+AACACGCT NW_026963474.1 24556 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 LH00469:254:22HGFVLT4:2:2258:6495:29198_1:N:0:TTGCGAAG+AACACGCT NW_026963734.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2267:30868:16759_1:N:0:TTGCGAAG+AACACGCT NW_026963604.1 1 Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2293:33644:3605_1:N:0:TTGCGAAG+AACACGCT NW_026963781.1 28258 Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2322:18940:4404_1:N:0:TTGCGAAG+AACACGCT NW_026963443.1 1 Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2361:21303:12164_1:N:0:TTGCGAAG+AACACGCT NW_026963741.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2361:21320:12164_1:N:0:TTGCGAAG+AACACGCT NW_026963741.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2361:21336:12164_1:N:0:TTGCGAAG+AACACGCT NW_026963741.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2361:21352:12164_1:N:0:TTGCGAAG+AACACGCT NW_026963741.1 1 Processed 56000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2411:26385:19840_1:N:0:TTGCGAAG+AACACGCT NW_026963352.1 336873 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2411:26393:19854_1:N:0:TTGCGAAG+AACACGCT NW_026963352.1 336873 Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2428:9812:28133_1:N:0:TTGCGAAG+AACACGCT NW_026963657.1 17829 Processed 61000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2446:3889:20121_1:N:0:TTGCGAAG+AACACGCT NW_026963443.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2447:11423:24897_1:N:0:TTGCGAAG+AACACGCT NW_026963487.1 25710 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2450:12418:8970_1:N:0:TTGCGAAG+AACACGCT NW_026963684.1 18445 Processed 62000000 sequence pairs so far Processed 63000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2470:4714:3227_1:N:0:TTGCGAAG+AACACGCT NW_026963377.1 2 Processed 64000000 sequence pairs so far Processed 65000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2496:23974:4516_1:N:0:TTGCGAAG+AACACGCT NW_026963483.1 1 Processed 66000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1125:41299:17697_1:N:0:TTGCGAAG+AACACGCT NW_026963443.1 56314 Processed 67000000 sequence pairs so far Processed 68000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1216:26474:24169_1:N:0:TTGCGAAG+AACACGCT NW_026963422.1 18032 Processed 69000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1233:12337:10231_1:N:0:TTGCGAAG+AACACGCT NW_026963422.1 18011 Processed 70000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1275:5459:14826_1:N:0:TTGCGAAG+AACACGCT NW_026963583.1 63462 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1285:16901:2275_1:N:0:TTGCGAAG+AACACGCT NW_026963771.1 24010 Processed 71000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1307:47603:5272_1:N:0:TTGCGAAG+AACACGCT NW_026963677.1 25090 Processed 72000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1355:20357:12711_1:N:0:TTGCGAAG+AACACGCT NW_026963616.1 36387 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1362:44900:13145_1:N:0:TTGCGAAG+AACACGCT NW_026963781.1 28257 Processed 73000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1391:46122:26830_1:N:0:TTGCGAAG+AACACGCT NW_026963394.1 2 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1401:35133:23637_1:N:0:TTGCGAAG+AACACGCT NW_026963743.1 1 Processed 74000000 sequence pairs so far Processed 75000000 sequence pairs so far Processed 76000000 sequence pairs so far Processed 77000000 sequence pairs so far Processed 78000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2166:25884:4012_1:N:0:TTGCGAAG+AACACGCT NW_026963326.1 1 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2168:11795:14980_1:N:0:TTGCGAAG+AACACGCT NW_026963443.1 56314 Processed 79000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2204:31111:10231_1:N:0:TTGCGAAG+AACACGCT NW_026963734.1 2 Processed 80000000 sequence pairs so far 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 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2438:37480:4278_1:N:0:TTGCGAAG+AACACGCT NW_026963684.1 18453 Processed 86000000 sequence pairs so far Processed 87000000 sequence pairs so far 87063380 reads; of these: 87063380 (100.00%) were paired; of these: 86982590 (99.91%) aligned concordantly 0 times 18353 (0.02%) aligned concordantly exactly 1 time 62437 (0.07%) aligned concordantly >1 times 0.09% overall alignment rate 87063380 reads; of these: 87063380 (100.00%) were paired; of these: 86983397 (99.91%) aligned concordantly 0 times 17520 (0.02%) aligned concordantly exactly 1 time 62463 (0.07%) aligned concordantly >1 times 0.09% overall alignment rate 87063380 reads; of these: 87063380 (100.00%) were paired; of these: 48756735 (56.00%) aligned concordantly 0 times 14962136 (17.19%) aligned concordantly exactly 1 time 23344509 (26.81%) aligned concordantly >1 times 44.00% overall alignment rate 87063380 reads; of these: 87063380 (100.00%) were paired; of these: 48772103 (56.02%) aligned concordantly 0 times 14944944 (17.17%) aligned concordantly exactly 1 time 23346333 (26.82%) aligned concordantly >1 times 43.98% overall alignment rate Processed 87063380 sequences in total Successfully deleted the temporary files 241M_1.fastq.gz_C_to_T.fastq, 241M_1.fastq.gz_G_to_A.fastq, 241M_2.fastq.gz_C_to_T.fastq and 241M_2.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 87063380 Final Cytosine Methylation Report ================================= Total number of C's analysed: 2019607327 Total methylated C's in CpG context: 31995729 Total methylated C's in CHG context: 9252856 Total methylated C's in CHH context: 46709944 Total methylated C's in Unknown context: 2338805 Total unmethylated C's in CpG context: 210560327 Total unmethylated C's in CHG context: 320559383 Total unmethylated C's in CHH context: 1400529088 Total unmethylated C's in Unknown context: 8790891 C methylated in CpG context: 13.2% C methylated in CHG context: 2.8% C methylated in CHH context: 3.2% C methylated in Unknown context (CN or CHN): 21.0% Bismark completed in 0d 5h 25m 38s ==================== Bismark run complete ====================