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/106M_1.fastq.gz ../data/raw-wgbs/106M_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/106M_1.fastq.gz and ../data/raw-wgbs/106M_2.fastq.gz Input files are in FastQ format Writing a C -> T converted version of the input file 106M_1.fastq.gz to 106M_1.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 106M_1.fastq.gz to 106M_1.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 106M_1.fastq.gz (88285661 sequences in total) Writing a C -> T converted version of the input file 106M_2.fastq.gz to 106M_2.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 106M_2.fastq.gz to 106M_2.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 106M_2.fastq.gz (88285661 sequences in total) Input files are 106M_1.fastq.gz_C_to_T.fastq and 106M_1.fastq.gz_G_to_A.fastq and 106M_2.fastq.gz_C_to_T.fastq and 106M_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 106M_1.fastq.gz_C_to_T.fastq and 106M_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: LH00469:254:22HGFVLT4:2:1101:3533:1014_1:N:0:AGCGTGTT+CTTCGCAA/1 99 NC_086377.1_CT_converted 70497283 6 151M = 70497425 293 TATATGAATATTTTTTAAAAAATGAAGATGAATTATAATGTGTTTTTTGTAATTGTAAGTATATTATTAAATATGTTTTAATTAATTGTATTGATTTTGTTGATATTTGTAAGAAGTATTTTAATGTTAATAATATGAATGATTTATTTAA IIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIII AS:i:-12 XS:i:-6 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:7G129T13 YS:i:-36 YT:Z:CP LH00469:254:22HGFVLT4:2:1101:3533:1014_2:N:0:AGCGTGTT+CTTCGCAA/2 147 NC_086377.1_CT_converted 70497425 6 151M = 70497283 -293 TTTATTTAATAATGTTTTATTTATAAATATTGTTGTTTTTTTAAAAGAAATTGGAATTTATTATAGAATATAAAAATGTTATTATATTGAAATTGATTTTAATTTTTATTATGTTATTTTATTGTTGATTTTTATTTTTTTTTTTTTTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-36 XS:i:-48 XN:i:0 XM:i:6 XO:i:0 XG:i:0 NM:i:6 MD:Z:138G1A1A1A3A0A1 YS:i:-12 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 106M_1.fastq.gz_G_to_A.fastq and 106M_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: LH00469:254:22HGFVLT4:2:1101:3533:1014_1:N:0:AGCGTGTT+CTTCGCAA/1 77 * 0 0 * * 0 0 TATATAAATATTTTTTAAAAAATAAAAATAAATTATAATATATTTTTTATAATTATAAATATATTATTAAATATATTTTAATTAATTATATTAATTTTATTAATATTTATAAAAAATATTTTAATATTAATAATATAAATAATTTATTTAA IIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00469:254:22HGFVLT4:2:1101:3533:1014_2:N:0:AGCGTGTT+CTTCGCAA/2 141 * 0 0 * * 0 0 GGAGGGAGGAAAAGAAATAAAAATTAATAATAAAATAATATAATAAAAATTAAAATTAATTTTAATATAATAATATTTTTATATTTTATAATAAATTTTAATTTTTTTTAAAAAAATAATAATATTTATAAATAAAATATTATTAAATAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 106M_1.fastq.gz_G_to_A.fastq and 106M_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: LH00469:254:22HGFVLT4:2:1101:3533:1014_1:N:0:AGCGTGTT+CTTCGCAA/1 77 * 0 0 * * 0 0 TATATAAATATTTTTTAAAAAATAAAAATAAATTATAATATATTTTTTATAATTATAAATATATTATTAAATATATTTTAATTAATTATATTAATTTTATTAATATTTATAAAAAATATTTTAATATTAATAATATAAATAATTTATTTAA IIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00469:254:22HGFVLT4:2:1101:3533:1014_2:N:0:AGCGTGTT+CTTCGCAA/2 141 * 0 0 * * 0 0 GGAGGGAGGAAAAGAAATAAAAATTAATAATAAAATAATATAATAAAAATTAAAATTAATTTTAATATAATAATATTTTTATATTTTATAATAAATTTTAATTTTTTTTAAAAAAATAATAATATTTATAAATAAAATATTATTAAATAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 106M_1.fastq.gz_C_to_T.fastq and 106M_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: LH00469:254:22HGFVLT4:2:1101:3533:1014_1:N:0:AGCGTGTT+CTTCGCAA/1 83 NW_026963295.1_GA_converted 4463939 6 151M = 4463797 -293 TTAAATAAATCATTCATATTATTAACATTAAAATACTTCTTACAAATATCAACAAAATCAATACAATTAATTAAAACATATTTAATAATATACTTACAATTACAAAAAACACATTATAATTCATCTTCATTTTTTAAAAAATATTCATATA IIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIII AS:i:-6 XS:i:-24 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:13A137 YS:i:-42 YT:Z:CP LH00469:254:22HGFVLT4:2:1101:3533:1014_2:N:0:AGCGTGTT+CTTCGCAA/2 163 NW_026963295.1_GA_converted 4463797 6 151M = 4463939 293 AAAAAAAAAAAAAAAAATAAAAATCAACAATAAAATAACATAATAAAAATTAAAATCAATTTCAATATAATAACATTTTTATATTCTATAATAAATTCCAATTTCTTTTAAAAAAACAACAATATTTATAAATAAAACATTATTAAATAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-42 XS:i:-42 XN:i:0 XM:i:7 XO:i:0 XG:i:0 NM:i:7 MD:Z:1T0T3T1T1T1C49A88 YS:i:-6 YT:Z:CP >>> Writing bisulfite mapping results to 106M_1_bismark_bt2_pe.bam <<< Reading in the sequence files ../data/raw-wgbs/106M_1.fastq.gz and ../data/raw-wgbs/106M_2.fastq.gz Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1105:22096:12949_1:N:0:AGCGTGTT+CTTCGCAA NW_026963309.1 1 Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1119:38799:29506_1:N:0:AGCGTGTT+CTTCGCAA NW_026963307.1 124855 Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1126:6754:11688_1:N:0:AGCGTGTT+CTTCGCAA NW_026963781.1 28256 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1128:34405:15344_1:N:0:AGCGTGTT+CTTCGCAA NW_026963362.1 2 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 LH00469:254:22HGFVLT4:2:1155:27980:24057_1:N:0:AGCGTGTT+CTTCGCAA NW_026963307.1 124855 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1158:38645:9012_1:N:0:AGCGTGTT+CTTCGCAA NW_026963783.1 1 Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1165:34639:7794_1:N:0:AGCGTGTT+CTTCGCAA NW_026963406.1 16944 Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1169:45151:20947_1:N:0:AGCGTGTT+CTTAGCAA NW_026963611.1 19968 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1170:35570:17277_1:N:0:AGCGTGTT+CTTCGCAA NW_026963498.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1175:31014:4768_1:N:0:AGCGTGTT+CTTCGCAA NW_026963659.1 21703 Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1181:23925:21830_1:N:0:AGCGTGTT+CTTCGCAA NW_026963402.1 95188 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1183:6284:25612_1:N:0:AGCGTGTT+CTTCGCAA NW_026963322.1 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 LH00469:254:22HGFVLT4:2:1209:12418:10511_1:N:0:AGCGTGTT+CTTCGCAA NW_026963585.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1210:4633:10315_1:N:0:AGCGTGTT+CTTCGCAA NW_026963322.1 898853 Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1218:40280:23020_1:N:0:AGCGTGTT+CTTCGCAA NW_026963404.1 32263 Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1227:51237:27951_1:N:0:CGCGTGTT+CTTCGCAA NW_026963443.1 56327 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1227:51228:27965_1:N:0:AGCGTGTT+CTTCGCAA NW_026963443.1 56327 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1227:51220:27979_1:N:0:AGCGTGTT+CTTCGCAA NW_026963443.1 56327 Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1283:22873:21157_1:N:0:AGCGTGTT+CTTCGCAA NW_026963443.1 56313 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1283:22889:21157_1:N:0:AGCGTGTT+CTTCGCAA NW_026963443.1 56313 Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1287:4083:11604_1:N:0:AGCGTGTT+CTTCGCAA NW_026963388.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1293:13017:11884_1:N:0:AGCGTGTT+CTTCGCAA NW_026963291.1 3 Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1307:15008:10511_1:N:0:AGCGTGTT+CTTCGCAA NW_026963335.1 1 Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1319:32268:16212_1:N:0:AGCGTGTT+CTTCGCAA NW_026963299.1 2 Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far 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 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1395:32786:21507_1:N:0:AGCGTGTT+CTTCGCAA NW_026963443.1 56330 Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1411:22509:8340_1:N:0:AGCGTGTT+CTTCGCAA NW_026963804.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1411:22525:8340_1:N:0:AGCGTGTT+CTTCGCAA NW_026963804.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1411:22533:8354_1:N:0:AGCGTGTT+CTTCGCAA NW_026963804.1 1 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 LH00469:254:22HGFVLT4:2:1430:1631:3802_1:N:0:AGCGTGTT+CTTCGCAA NW_026963667.1 1 Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1471:36169:8536_1:N:0:AGCGTGTT+CTTCGCAA NW_026963585.1 2 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 LH00469:254:22HGFVLT4:2:2112:24184:24631_1:N:0:AGCGTGTT+CTTCGCAA NW_026963552.1 47121 Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2150:33854:18762_1:N:0:AGCGTGTT+CTTCGCAA NW_026963470.1 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 Processed 56000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2192:18010:11254_1:N:0:AGCGTGTT+CTTCGCAA NW_026963631.1 26225 Processed 57000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2203:44326:29688_1:N:0:AGCGTGTT+CTTCGCAA NW_026963402.1 95188 Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2222:29444:11828_1:N:0:AGCGTGTT+CTTCGCAA NW_026963585.1 2 Processed 60000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2231:34534:19154_1:N:0:AGCGTGTT+CTTCGCAA NW_026963411.1 26100 Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far 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 LH00469:254:22HGFVLT4:2:2280:42983:14251_1:N:0:AGCGTGTT+CTTCGCAA NW_026963589.1 26175 Processed 66000000 sequence pairs so far Processed 67000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2298:5993:4152_1:N:0:AGCGTGTT+CTTCGCAA NW_026963402.1 95195 Processed 68000000 sequence pairs so far Processed 69000000 sequence pairs so far Processed 70000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2325:37067:3760_1:N:0:AGCGTGTT+CTTCGCAA NW_026963299.1 2 Processed 71000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2339:45046:17739_1:N:0:AGCGTGTT+CTTCGCAA NW_026963317.1 4467275 Processed 72000000 sequence pairs so far Processed 73000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2350:29161:23272_1:N:0:AGCGTGTT+CTTCGCAA NW_026963326.1 1 Processed 74000000 sequence pairs so far Processed 75000000 sequence pairs so far Processed 76000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2380:19774:22376_1:N:0:AGCGTGTT+CTTCGCAA NW_026963377.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2383:23747:22110_1:N:0:AGCGTGTT+CTTCGCAA NW_026963743.1 1 Processed 77000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2398:1834:12416_1:N:0:AGCGTGTT+CTTCGCAA NW_026963299.1 2 Processed 78000000 sequence pairs so far Processed 79000000 sequence pairs so far Processed 80000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2429:16319:25191_1:N:0:AGCGTGTT+CTTCGCAA NW_026963675.1 19994 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2429:16327:25233_1:N:0:AGCGTGTT+CTTCGCAA NW_026963675.1 19994 Processed 81000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2431:20923:20891_1:N:0:AGCGTGTT+CTTCGCAA NW_026963516.1 2 Processed 82000000 sequence pairs so far Processed 83000000 sequence pairs so far Processed 84000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2460:24953:9153_1:N:0:AGCGTGTT+CTTCGCCA NW_026963585.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2460:24945:9167_1:N:0:AGCGTGTT+CTTCGCAA NW_026963585.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2460:24961:9167_1:N:0:AGCGTGTT+CTTCGCAA NW_026963585.1 2 Processed 85000000 sequence pairs so far Processed 86000000 sequence pairs so far Processed 87000000 sequence pairs so far Processed 88000000 sequence pairs so far 88285661 reads; of these: 88285661 (100.00%) were paired; of these: 52021449 (58.92%) aligned concordantly 0 times 15416478 (17.46%) aligned concordantly exactly 1 time 20847734 (23.61%) aligned concordantly >1 times 41.08% overall alignment rate 88285661 reads; of these: 88285661 (100.00%) were paired; of these: 52036868 (58.94%) aligned concordantly 0 times 15414793 (17.46%) aligned concordantly exactly 1 time 20834000 (23.60%) aligned concordantly >1 times 41.06% overall alignment rate 88285661 reads; of these: 88285661 (100.00%) were paired; of these: 88220413 (99.93%) aligned concordantly 0 times 20673 (0.02%) aligned concordantly exactly 1 time 44575 (0.05%) aligned concordantly >1 times 0.07% overall alignment rate 88285661 reads; of these: 88285661 (100.00%) were paired; of these: 88222275 (99.93%) aligned concordantly 0 times 20083 (0.02%) aligned concordantly exactly 1 time 43303 (0.05%) aligned concordantly >1 times 0.07% overall alignment rate Processed 88285661 sequences in total Successfully deleted the temporary files 106M_1.fastq.gz_C_to_T.fastq, 106M_1.fastq.gz_G_to_A.fastq, 106M_2.fastq.gz_C_to_T.fastq and 106M_2.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 88285661 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1962807409 Total methylated C's in CpG context: 31979766 Total methylated C's in CHG context: 9086543 Total methylated C's in CHH context: 44917378 Total methylated C's in Unknown context: 2178645 Total unmethylated C's in CpG context: 191761640 Total unmethylated C's in CHG context: 305459310 Total unmethylated C's in CHH context: 1379602772 Total unmethylated C's in Unknown context: 8586471 C methylated in CpG context: 14.3% C methylated in CHG context: 2.9% C methylated in CHH context: 3.2% C methylated in Unknown context (CN or CHN): 20.2% Bismark completed in 0d 4h 49m 35s ==================== Bismark run complete ====================