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/107M_1.fastq.gz ../data/raw-wgbs/107M_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/107M_1.fastq.gz and ../data/raw-wgbs/107M_2.fastq.gz Input files are in FastQ format Writing a C -> T converted version of the input file 107M_1.fastq.gz to 107M_1.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 107M_1.fastq.gz to 107M_1.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 107M_1.fastq.gz (94606480 sequences in total) Writing a C -> T converted version of the input file 107M_2.fastq.gz to 107M_2.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 107M_2.fastq.gz to 107M_2.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 107M_2.fastq.gz (94606480 sequences in total) Input files are 107M_1.fastq.gz_C_to_T.fastq and 107M_1.fastq.gz_G_to_A.fastq and 107M_2.fastq.gz_C_to_T.fastq and 107M_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 107M_1.fastq.gz_C_to_T.fastq and 107M_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: LH00469:254:22HGFVLT4:2:1101:1898:1014_1:N:0:GATCGAGT+GACGAACT/1 77 * 0 0 * * 0 0 TTATTTATATTGTTATTTTGTTAATTATTTATTTTGTTATTTTGATATATTTATATTGTTATTTTGATATTTAAATTGTTATATTGATATATTTATTTTGTTATTTTGATATTTAAATTGTAATATTGATATATTTATTTTGTTATTTTGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII9IIIIIIIII9IIIIIIIIIIIIIIIIII YT:Z:UP LH00469:254:22HGFVLT4:2:1101:1898:1014_2:N:0:GATCGAGT+GACGAACT/2 141 * 0 0 * * 0 0 AAAAATACACCACATATATATCAAAATAACAATATAATTATATCAAAATAACAAAATAAATATATCAATATTACAATTTAAATATCAAAATAACAAAATAAATATATCAATATAACAATTTAAATATCAAAATAACAATATAAATATATCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II9II9IIIII9IIIIIIIIIIIIIII9 YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 107M_1.fastq.gz_G_to_A.fastq and 107M_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: LH00469:254:22HGFVLT4:2:1101:1898:1014_1:N:0:GATCGAGT+GACGAACT/1 77 * 0 0 * * 0 0 TTATTTATATTATTATTTTATTAATTATTTATTTTATTATTTTAATATATTTATATTATTATTTTAATATTTAAATTATTATATTAATATATTTATTTTATTATTTTAATATTTAAATTATAATATTAATATATTTATTTTATTATTTTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII9IIIIIIIII9IIIIIIIIIIIIIIIIII YT:Z:UP LH00469:254:22HGFVLT4:2:1101:1898:1014_2:N:0:GATCGAGT+GACGAACT/2 141 * 0 0 * * 0 0 GGGGATATATTATATATATATTAAAATAATAATATAATTATATTAAAATAATAAAATAAATATATTAATATTATAATTTAAATATTAAAATAATAAAATAAATATATTAATATAATAATTTAAATATTAAAATAATAATATAAATATATTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II9II9IIIII9IIIIIIIIIIIIIII9 YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 107M_1.fastq.gz_G_to_A.fastq and 107M_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: LH00469:254:22HGFVLT4:2:1101:1898:1014_1:N:0:GATCGAGT+GACGAACT/1 77 * 0 0 * * 0 0 TTATTTATATTATTATTTTATTAATTATTTATTTTATTATTTTAATATATTTATATTATTATTTTAATATTTAAATTATTATATTAATATATTTATTTTATTATTTTAATATTTAAATTATAATATTAATATATTTATTTTATTATTTTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII9IIIIIIIII9IIIIIIIIIIIIIIIIII YT:Z:UP LH00469:254:22HGFVLT4:2:1101:1898:1014_2:N:0:GATCGAGT+GACGAACT/2 141 * 0 0 * * 0 0 GGGGATATATTATATATATATTAAAATAATAATATAATTATATTAAAATAATAAAATAAATATATTAATATTATAATTTAAATATTAAAATAATAAAATAAATATATTAATATAATAATTTAAATATTAAAATAATAATATAAATATATTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II9II9IIIII9IIIIIIIIIIIIIII9 YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 107M_1.fastq.gz_C_to_T.fastq and 107M_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: LH00469:254:22HGFVLT4:2:1101:1898:1014_1:N:0:GATCGAGT+GACGAACT/1 77 * 0 0 * * 0 0 TTATTTATATTGTTATTTTGTTAATTATTTATTTTGTTATTTTGATATATTTATATTGTTATTTTGATATTTAAATTGTTATATTGATATATTTATTTTGTTATTTTGATATTTAAATTGTAATATTGATATATTTATTTTGTTATTTTGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII9IIIIIIIII9IIIIIIIIIIIIIIIIII YT:Z:UP LH00469:254:22HGFVLT4:2:1101:1898:1014_2:N:0:GATCGAGT+GACGAACT/2 141 * 0 0 * * 0 0 AAAAATACACCACATATATATCAAAATAACAATATAATTATATCAAAATAACAAAATAAATATATCAATATTACAATTTAAATATCAAAATAACAAAATAAATATATCAATATAACAATTTAAATATCAAAATAACAATATAAATATATCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II9II9IIIII9IIIIIIIIIIIIIII9 YT:Z:UP >>> Writing bisulfite mapping results to 107M_1_bismark_bt2_pe.bam <<< Reading in the sequence files ../data/raw-wgbs/107M_1.fastq.gz and ../data/raw-wgbs/107M_2.fastq.gz Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1115:14983:21059_1:N:0:GATCGAGT+GACGAACT NW_026963611.1 19968 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1121:45297:7752_1:N:0:GATCGAGT+GACGAACT NW_026963443.1 56331 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1126:44666:4922_1:N:0:GATCGAGT+GACGAACT NC_086374.1 103707506 Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1132:37083:9755_1:N:0:GATCGAGT+GACGAACT NW_026963743.1 1 Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1153:43177:12150_1:N:0:GATCGAGT+GACGAACT NW_026963585.1 2 Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1159:16375:27811_1:N:0:GATCGAGT+GACGAACT NW_026963360.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1161:26693:19028_1:N:0:GATCGAGT+GACGAACT NW_026963772.1 22148 Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1166:49926:28875_1:N:0:GATCGAGT+GACGAACT NW_026963743.1 1 Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1174:24654:15386_1:N:0:GATCGAGT+GACGAACT NW_026963372.1 501095 Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1204:31807:24743_1:N:0:GATCGAGT+GACGAACT NW_026963743.1 1 Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1251:13834:21535_1:N:0:GATCGAGT+GACGAACT NW_026963462.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1251:13842:21549_1:N:0:GATCGAGT+GACGAACT NW_026963462.1 1 Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1253:45710:21998_1:N:0:GATCGAGT+GACGAACT NW_026963634.1 1 Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1269:10249:19868_1:N:0:GATCGAGT+GACGAACT NW_026963354.1 1 Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1277:40992:25149_1:N:0:GATCGAGT+GACGAACT NW_026963377.1 2 Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1281:9100:20653_1:N:0:GATCGAGT+GACGAACT NW_026963743.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1287:17452:6281_1:N:0:GATCGAGT+GACGAACT NW_026963443.1 1 Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1307:6859:7948_1:N:0:GATCGAGT+GACGAACT NW_026963778.1 1 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 LH00469:254:22HGFVLT4:2:1327:38111:15064_1:N:0:GATCGAGT+GACGAACT NW_026963743.1 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 LH00469:254:22HGFVLT4:2:1359:11034:3746_1:N:0:GATCGAGT+GACGAACT NW_026963778.1 1 Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1380:31961:11506_1:N:0:GATCGAGT+GACGAACT NW_026963411.1 26097 Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1386:21781:22348_1:N:0:GATCGAGT+GACGAACT NW_026963319.1 1 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 Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1470:29541:22278_1:N:0:GATCGAGT+GACGAACT NW_026963372.1 501095 Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1486:41712:28049_1:N:0:GATCGAGT+GACGAACT NW_026963603.1 20008 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1490:1753:3928_1:N:0:GATCGAGT+GACGAACT NW_026963516.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1491:31289:27545_1:N:0:GATCGAGT+GACGAACT NW_026963659.1 21704 Processed 43000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2102:9829:22138_1:N:0:GATCGAGT+GACGAACT NW_026963743.1 1 Processed 44000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2107:33167:6841_1:N:0:GATCGAGT+GACGAACT NW_026963388.1 1 Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far 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 LH00469:254:22HGFVLT4:2:2167:39592:22978_1:N:0:GATCGAGT+GACGAACT NW_026963743.1 1 Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2188:13324:15386_1:N:0:GATCGAGT+GACGAACT NW_026963667.1 1 Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 57000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2230:28052:20373_1:N:0:GATCGAGT+GACGAACT NW_026963443.1 56309 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2230:28060:20387_1:N:0:GATCGAGT+GACGAACT NW_026963443.1 56309 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2230:28069:20401_1:N:0:GATCGAGT+GACGAACT NW_026963443.1 56309 Processed 58000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2241:18188:9937_1:N:0:GATCGAGT+GACGAACT NW_026963411.1 26092 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2241:44892:10301_1:N:0:GATCGAGT+GACGAACT NW_026963692.1 27301 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2248:49424:3886_1:N:0:GATCGAGT+GACGAACT NW_026963443.1 56339 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2248:49416:3900_1:N:0:GATCGAGT+GACGAACT NW_026963443.1 56339 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2248:43978:18804_1:N:0:GATCGAGT+GACGAACT NW_026963334.1 25255 Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2262:41089:11618_1:N:0:GATCGAGT+GACGAACT NW_026963743.1 1 Processed 61000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2269:20001:9012_1:N:0:GATCGAGT+GACGAACT NW_026963533.1 25092 Processed 62000000 sequence pairs so far Processed 63000000 sequence pairs so far Processed 64000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2307:42934:13971_1:N:0:GATCGAGT+GACGAACT NW_026963443.1 56334 Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 67000000 sequence pairs so far Processed 68000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2340:45030:28497_1:N:0:GATCGAGT+GACGAACT NW_026963684.1 18465 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2341:10614:23160_1:N:0:GATCGAGT+GACGAACT NW_026963404.1 32247 Processed 69000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2353:6001:27139_1:N:0:GATCGAGT+GACGAACT NW_026963743.1 1 Processed 70000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2361:25010:19448_1:N:0:GATTGAGT+GACGAACT NW_026963404.1 2 Processed 71000000 sequence pairs so far Processed 72000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2381:14085:24239_1:N:0:GATCGAGT+GACGAACT NW_026963443.1 56330 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2384:25746:27755_1:N:0:GATCGAGT+GACGAACT NW_026963743.1 1 Processed 73000000 sequence pairs so far 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 LH00469:254:22HGFVLT4:2:2442:18924:23679_1:N:0:GATCGAGT+GACGAACT NW_026963743.1 1 Processed 79000000 sequence pairs so far Processed 80000000 sequence pairs so far Processed 81000000 sequence pairs so far Processed 82000000 sequence pairs so far Processed 83000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2498:11099:4362_1:N:0:GATCGAGT+GACGAACT NW_026963418.1 81274 Processed 84000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1153:51123:19042_1:N:0:GATCGAGT+GACGAACT NW_026963443.1 2 Processed 85000000 sequence pairs so far Processed 86000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1269:28999:27223_1:N:0:GATCGAGT+GACGAACT NW_026963585.1 2 Processed 87000000 sequence pairs so far Processed 88000000 sequence pairs so far Processed 89000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1492:24152:15946_1:N:0:GATCGAGT+GACGAACT NW_026963743.1 1 Processed 90000000 sequence pairs so far Processed 91000000 sequence pairs so far Processed 92000000 sequence pairs so far Processed 93000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2456:49392:23132_1:N:0:GATCGAGT+GACGAACT NW_026963319.1 1 Processed 94000000 sequence pairs so far 94606480 reads; of these: 94606480 (100.00%) were paired; of these: 56005429 (59.20%) aligned concordantly 0 times 16526405 (17.47%) aligned concordantly exactly 1 time 22074646 (23.33%) aligned concordantly >1 times 40.80% overall alignment rate 94606480 reads; of these: 94606480 (100.00%) were paired; of these: 94531360 (99.92%) aligned concordantly 0 times 23984 (0.03%) aligned concordantly exactly 1 time 51136 (0.05%) aligned concordantly >1 times 0.08% overall alignment rate 94606480 reads; of these: 94606480 (100.00%) were paired; of these: 94534147 (99.92%) aligned concordantly 0 times 23257 (0.02%) aligned concordantly exactly 1 time 49076 (0.05%) aligned concordantly >1 times 0.08% overall alignment rate 94606480 reads; of these: 94606480 (100.00%) were paired; of these: 56005046 (59.20%) aligned concordantly 0 times 16519794 (17.46%) aligned concordantly exactly 1 time 22081640 (23.34%) aligned concordantly >1 times 40.80% overall alignment rate Processed 94606480 sequences in total Successfully deleted the temporary files 107M_1.fastq.gz_C_to_T.fastq, 107M_1.fastq.gz_G_to_A.fastq, 107M_2.fastq.gz_C_to_T.fastq and 107M_2.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 94606480 Final Cytosine Methylation Report ================================= Total number of C's analysed: 2094009985 Total methylated C's in CpG context: 34685592 Total methylated C's in CHG context: 9789192 Total methylated C's in CHH context: 48499355 Total methylated C's in Unknown context: 2443577 Total unmethylated C's in CpG context: 204295251 Total unmethylated C's in CHG context: 325425456 Total unmethylated C's in CHH context: 1471315139 Total unmethylated C's in Unknown context: 9298891 C methylated in CpG context: 14.5% C methylated in CHG context: 2.9% C methylated in CHH context: 3.2% C methylated in Unknown context (CN or CHN): 20.8% Bismark completed in 0d 5h 22m 34s ==================== Bismark run complete ====================