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/109M_1.fastq.gz ../data/raw-wgbs/109M_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/109M_1.fastq.gz and ../data/raw-wgbs/109M_2.fastq.gz Input files are in FastQ format Writing a C -> T converted version of the input file 109M_1.fastq.gz to 109M_1.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 109M_1.fastq.gz to 109M_1.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 109M_1.fastq.gz (93271100 sequences in total) Writing a C -> T converted version of the input file 109M_2.fastq.gz to 109M_2.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 109M_2.fastq.gz to 109M_2.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 109M_2.fastq.gz (93271100 sequences in total) Input files are 109M_1.fastq.gz_C_to_T.fastq and 109M_1.fastq.gz_G_to_A.fastq and 109M_2.fastq.gz_C_to_T.fastq and 109M_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 109M_1.fastq.gz_C_to_T.fastq and 109M_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: LH00469:254:22HGFVLT4:2:1101:1332:1014_1:N:0:ACAGATCA+TACTGCTC/1 77 * 0 0 * * 0 0 ATAGTTATATTGTTGAATTAGATAAATAGTTAAAATTTATATATTGATATGTTTTGTGTTTTTTTTTATATTGTTTTGAATTTTAAGTATGTTGTTTTTATTGATTTTTTTATTTTTGTATTTTTTTAATTGGAAGAATATAAATTTAAAT II9-9II999IIII9IIIII-II9II-IIII9II-II-9III-I9-I-III9III9IIII-I9I9-I-I-III--IIIIII-9II9I-9II---9999---9-99---9I--999--99-9999999-9-I99-----9--9----9-999 YT:Z:UP LH00469:254:22HGFVLT4:2:1101:1332:1014_2:N:0:ACAGATCA+TACTGCTC/2 141 * 0 0 * * 0 0 AAAAAATACAAAAATAAAAAACTCAATAAAAATAACATACTTAATATTCAATCCAATATAAAACAAAACACAAAACATATCAATATCTAACTTCCAACTATTTATCTAATTCAACAATATAACTATAAATCAAAAAAACATCATATAAAAA IIII--IIIIIII9II-II9--IIII9I9II9-9IIIIIIIIIIIIIIII-IIII9-I9I9I--9IIIIIIIII-II99IIIIIII-I9I-I9--999I9-III-9I99II9I99IIIII9II9III9III-I9II9III9-I9I--I-I- YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from 109M_1.fastq.gz_G_to_A.fastq and 109M_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: LH00469:254:22HGFVLT4:2:1101:1332:1014_1:N:0:ACAGATCA+TACTGCTC/1 77 * 0 0 * * 0 0 ATAATTACATTATTAAATTAAATAAATAATTAAAATTTATATATTAATATATTTTATATTTTTTTTTATATTATCTTAAATCTTAAATATATTATTTTTATTAACTTTTTTATTTTCATACCCCTCCAATCAAAAAAACACAAACCTAAAC II9-9II999IIII9IIIII-II9II-IIII9II-II-9III-I9-I-III9III9IIII-I9I9-I-I-III--IIIIII-9II9I-9II---9999---9-99---9I--999--99-9999999-9-I99-----9--9----9-999 YT:Z:UP LH00469:254:22HGFVLT4:2:1101:1332:1014_2:N:0:ACAGATCA+TACTGCTC/2 141 * 0 0 * * 0 0 GAGGGGTATAAAAATAAAAAATTTAATAAAAATAATATATTTAATATTTAATTTAATATAAAATAAAATATAAAATATATTAATATTTAATTTTTAATTATTTATTTAATTTAATAATATAATTATAGATTGGAAGAGTGTTGTGTAGGGA IIII--IIIIIII9II-II9--IIII9I9II9-9IIIIIIIIIIIIIIII-IIII9-I9I9I--9IIIIIIIII-II99IIIIIII-I9I-I9--999I9-III-9I99II9I99IIIII9II9III9III-I9II9III9-I9I--I-I- YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from 109M_1.fastq.gz_G_to_A.fastq and 109M_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: LH00469:254:22HGFVLT4:2:1101:1332:1014_1:N:0:ACAGATCA+TACTGCTC/1 77 * 0 0 * * 0 0 ATAATTACATTATTAAATTAAATAAATAATTAAAATTTATATATTAATATATTTTATATTTTTTTTTATATTATCTTAAATCTTAAATATATTATTTTTATTAACTTTTTTATTTTCATACCCCTCCAATCAAAAAAACACAAACCTAAAC II9-9II999IIII9IIIII-II9II-IIII9II-II-9III-I9-I-III9III9IIII-I9I9-I-I-III--IIIIII-9II9I-9II---9999---9-99---9I--999--99-9999999-9-I99-----9--9----9-999 YT:Z:UP LH00469:254:22HGFVLT4:2:1101:1332:1014_2:N:0:ACAGATCA+TACTGCTC/2 141 * 0 0 * * 0 0 GAGGGGTATAAAAATAAAAAATTTAATAAAAATAATATATTTAATATTTAATTTAATATAAAATAAAATATAAAATATATTAATATTTAATTTTTAATTATTTATTTAATTTAATAATATAATTATAGATTGGAAGAGTGTTGTGTAGGGA IIII--IIIIIII9II-II9--IIII9I9II9-9IIIIIIIIIIIIIIII-IIII9-I9I9I--9IIIIIIIII-II99IIIIIII-I9I-I9--999I9-III-9I99II9I99IIIII9II9III9III-I9II9III9-I9I--I-I- YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 109M_1.fastq.gz_C_to_T.fastq and 109M_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: LH00469:254:22HGFVLT4:2:1101:1332:1014_1:N:0:ACAGATCA+TACTGCTC/1 77 * 0 0 * * 0 0 ATAGTTATATTGTTGAATTAGATAAATAGTTAAAATTTATATATTGATATGTTTTGTGTTTTTTTTTATATTGTTTTGAATTTTAAGTATGTTGTTTTTATTGATTTTTTTATTTTTGTATTTTTTTAATTGGAAGAATATAAATTTAAAT II9-9II999IIII9IIIII-II9II-IIII9II-II-9III-I9-I-III9III9IIII-I9I9-I-I-III--IIIIII-9II9I-9II---9999---9-99---9I--999--99-9999999-9-I99-----9--9----9-999 YT:Z:UP LH00469:254:22HGFVLT4:2:1101:1332:1014_2:N:0:ACAGATCA+TACTGCTC/2 141 * 0 0 * * 0 0 AAAAAATACAAAAATAAAAAACTCAATAAAAATAACATACTTAATATTCAATCCAATATAAAACAAAACACAAAACATATCAATATCTAACTTCCAACTATTTATCTAATTCAACAATATAACTATAAATCAAAAAAACATCATATAAAAA IIII--IIIIIII9II-II9--IIII9I9II9-9IIIIIIIIIIIIIIII-IIII9-I9I9I--9IIIIIIIII-II99IIIIIII-I9I-I9--999I9-III-9I99II9I99IIIII9II9III9III-I9II9III9-I9I--I-I- YT:Z:UP >>> Writing bisulfite mapping results to 109M_1_bismark_bt2_pe.bam <<< Reading in the sequence files ../data/raw-wgbs/109M_1.fastq.gz and ../data/raw-wgbs/109M_2.fastq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1122:29307:6911_1:N:0:ACAGCTCA+TACTGCTC NW_026963743.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1125:45540:3942_1:N:0:ACAGCTCA+TACTGCTC NW_026963771.1 24006 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1128:41469:6785_1:N:0:ACAGCTCA+TACTGCTC NC_086381.1 82294976 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1128:42230:12192_1:N:0:ACAGCTCA+TACTGCTC NW_026963767.1 2 Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1136:25155:19700_1:N:0:ACAGCTCA+TACTGCTC NW_026963743.1 1 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1144:15865:19560_1:N:0:ACAGCTCA+TACTGCTC NW_026963781.1 28274 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1146:21716:16212_1:N:0:ACAGCTCA+TACTGCTC NW_026963550.1 42753 Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1158:26240:8298_1:N:0:ACAGCTCA+TACTGCTC NW_026963428.1 29768 Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1161:6665:13047_1:N:0:ACAGCTCA+TACTGCTC NW_026963404.1 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 LH00469:254:22HGFVLT4:2:1191:44277:13691_1:N:0:ACAGCTCA+TACTGCTC NW_026963322.1 898853 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1191:44293:13691_1:N:0:ACAGCTCA+TACTGCTC NW_026963322.1 898853 Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1234:13025:12346_1:N:0:ACAGCTCA+TACTGCTC NW_026963684.1 18444 Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1240:31840:26844_1:N:0:ACAGCTCA+TACTGCTC NW_026963749.1 18238 Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1267:49731:1981_1:N:0:ACAGCTCA+TACTGCTC NW_026963345.1 224328 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 LH00469:254:22HGFVLT4:2:1288:6770:15162_1:N:0:ACAGCTCA+TACTGCTC NW_026963307.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1294:25989:25570_1:N:0:ACAGCTCA+TACTGCTC NW_026963743.1 1 Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1308:4180:21493_1:N:0:ACAGCTCA+TACTGCTC NW_026963768.1 22272 Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1325:32349:12094_1:N:0:ACAGCTCA+TACTGCTC NW_026963717.1 35365 Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1343:16440:12795_1:N:0:ACAGCTCA+TACTGCTC NW_026963777.1 1 Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1351:27599:25219_1:N:0:ACAGCTCA+TACTGCTC NW_026963554.1 2 Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1364:48064:4782_1:N:0:CCAGCTCA+TACTGCTC NW_026963462.1 1 Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1395:35772:9447_1:N:0:ACAGCTCA+TACTGCTC NW_026963710.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1397:29121:6729_1:N:0:ACAGCTCA+TACTGCTC NW_026963319.1 1 Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1424:5645:28567_1:N:0:ACAGCTCA+TACTGCTC NW_026963717.1 35387 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1426:31233:23440_1:N:0:ACAGCTCA+TACTGCTC NW_026963362.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1429:21473:22516_1:N:0:ACAGCTCA+TACTGCTC NW_026963481.1 22904 Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1434:12928:15008_1:N:0:ACAGCTCA+TACTGCTC NW_026963443.1 56316 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1434:12944:15008_1:N:0:ACAGCTCA+TACTGCTC NW_026963443.1 56316 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1434:12936:15022_1:N:0:ACAGCTCA+TACTGCTC NW_026963443.1 56316 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1435:31581:26200_1:N:0:ACAGCTCA+TACTGCTC NW_026963771.1 24008 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 LH00469:254:22HGFVLT4:2:2107:2732:27951_1:N:0:ACAGCTCA+TACTGCTC NW_026963399.1 1 Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2141:43233:24575_1:N:0:ACAGCTCA+TACTGCTC NW_026963347.1 1227468 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 LH00469:254:22HGFVLT4:2:2181:7134:10105_1:N:0:ACAGCTCA+TACTGCTC NW_026963298.1 2989476 Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2239:3590:6099_1:N:0:ACAGCTCA+TACTGCTC NW_026963743.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2244:52078:4110_1:N:0:ACAGCTCA+TACTGCTC NW_026963443.1 1 Processed 53000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2245:28028:21059_1:N:0:ACAGCTCA+TACTGCTC NW_026963319.1 1 Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2269:13324:5496_1:N:0:ACAGCTCA+TACTGCTC NW_026963550.1 42751 Processed 56000000 sequence pairs so far 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 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2335:7288:2387_1:N:0:ACAGCTCA+TACTGCTC NW_026963308.1 2 Processed 62000000 sequence pairs so far Processed 63000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2354:46033:13985_1:N:0:ACAGCTCA+TACTGCTC NW_026963307.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2354:46025:13999_1:N:0:ACAGCTCA+TACTGCTC NW_026963307.1 1 Processed 64000000 sequence pairs so far 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 LH00469:254:22HGFVLT4:2:2420:51601:11744_1:N:0:ACAGCTCA+TACTGCTC NW_026963743.1 1 Processed 69000000 sequence pairs so far Processed 70000000 sequence pairs so far Processed 71000000 sequence pairs so far Processed 72000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2457:2343:4810_1:N:0:ACAGCTCA+TACTGCTC NW_026963377.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2457:2351:4824_1:N:0:ACAGCTCA+TACTGCTC NW_026963377.1 2 Processed 73000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2469:22687:16913_1:N:0:ACAGCTCN+TACTGCTC NW_026963377.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2472:37488:25752_1:N:0:ACAGCTCA+TACTGCTC NW_026963551.1 28440 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2472:37480:25766_1:N:0:ACAGCTCA+TACTGCTC NW_026963551.1 28440 Processed 74000000 sequence pairs so far Processed 75000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2488:15178:15568_1:N:0:ACAGCTCA+TACTGCTC NW_026963563.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2488:39074:18580_1:N:0:ACAGCTCA+TACTGCTC NW_026963636.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2492:11479:17291_1:N:0:ACAGCTCA+TACTGCTC NW_026963307.1 1 Processed 76000000 sequence pairs so far Processed 77000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1182:47093:6463_1:N:0:ACAGCTCA+TACTGCTC NW_026963743.1 1 Processed 78000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1228:20276:6183_1:N:0:ACAGCTCA+TACTGCTC NW_026963443.1 1 Processed 79000000 sequence pairs so far Processed 80000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1288:14894:21886_1:N:0:ACAGCTCA+TACTGCTC NW_026963404.1 1 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1289:31208:28525_1:N:0:ACAGCTCA+TACTGCTC NW_026963564.1 18990 Processed 81000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1339:23278:2107_1:N:0:ACAGCTCA+TACTGCTC NW_026963397.1 22662 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1349:35271:20877_1:N:0:ACAGCTCC+TACTGCTC NW_026963331.1 1 Processed 82000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1398:35068:25374_1:N:0:ACAGCTCA+TACTGCTC NW_026963564.1 18992 Processed 83000000 sequence pairs so far Processed 84000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1494:12159:17011_1:N:0:ACAGCTCA+TACTGCTC NW_026963585.1 2 Processed 85000000 sequence pairs so far Processed 86000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2168:20955:4978_1:N:0:ACAGCTCA+TACTGCTC NW_026963307.1 124866 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2181:18188:4026_1:N:0:ACAGCTCA+TACTGCTC NW_026963322.1 898846 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 LH00586:122:22HTFTLT4:7:2317:49561:16675_1:N:0:ACAGCTCA+TACTGCTC 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 93271100 reads; of these: 93271100 (100.00%) were paired; of these: 54903736 (58.86%) aligned concordantly 0 times 16385007 (17.57%) aligned concordantly exactly 1 time 21982357 (23.57%) aligned concordantly >1 times 41.14% overall alignment rate 93271100 reads; of these: 93271100 (100.00%) were paired; of these: 54895531 (58.86%) aligned concordantly 0 times 16380672 (17.56%) aligned concordantly exactly 1 time 21994897 (23.58%) aligned concordantly >1 times 41.14% overall alignment rate 93271100 reads; of these: 93271100 (100.00%) were paired; of these: 93190620 (99.91%) aligned concordantly 0 times 22645 (0.02%) aligned concordantly exactly 1 time 57835 (0.06%) aligned concordantly >1 times 0.09% overall alignment rate 93271100 reads; of these: 93271100 (100.00%) were paired; of these: 93191956 (99.92%) aligned concordantly 0 times 22223 (0.02%) aligned concordantly exactly 1 time 56921 (0.06%) aligned concordantly >1 times 0.08% overall alignment rate Processed 93271100 sequences in total Successfully deleted the temporary files 109M_1.fastq.gz_C_to_T.fastq, 109M_1.fastq.gz_G_to_A.fastq, 109M_2.fastq.gz_C_to_T.fastq and 109M_2.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 93271100 Final Cytosine Methylation Report ================================= Total number of C's analysed: 2087963570 Total methylated C's in CpG context: 33633247 Total methylated C's in CHG context: 9624140 Total methylated C's in CHH context: 47818812 Total methylated C's in Unknown context: 2283892 Total unmethylated C's in CpG context: 205848479 Total unmethylated C's in CHG context: 325770817 Total unmethylated C's in CHH context: 1465268075 Total unmethylated C's in Unknown context: 9119364 C methylated in CpG context: 14.0% C methylated in CHG context: 2.9% C methylated in CHH context: 3.2% C methylated in Unknown context (CN or CHN): 20.0% Bismark completed in 0d 5h 22m 41s ==================== Bismark run complete ====================