Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.5.2]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/modules/uri_apps/software/SAMtools/1.14-GCC-11.2.0/bin/samtools' Reference genome folder provided is ../data/ (absolute path is '/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/data/)' FastQ format assumed (by default) Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Each Bowtie 2 instance is going to be run with 48 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/code'): ../output/01.00-D-Apul-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_ACR-178-TP2_S1_R1_001.fastq.gz ../output/01.00-D-Apul-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_ACR-178-TP2_S1_R2_001.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: /scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/ Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-1.0 -p 48 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/code Now reading in and storing sequence information of the genome specified in: /scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/data/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are ../output/01.00-D-Apul-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_ACR-178-TP2_S1_R1_001.fastq.gz and ../output/01.00-D-Apul-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_ACR-178-TP2_S1_R2_001.fastq.gz Input files are in FastQ format Writing a C -> T converted version of the input file trimmed_ACR-178-TP2_S1_R1_001.fastq.gz to trimmed_ACR-178-TP2_S1_R1_001.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file trimmed_ACR-178-TP2_S1_R1_001.fastq.gz to trimmed_ACR-178-TP2_S1_R1_001.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file trimmed_ACR-178-TP2_S1_R1_001.fastq.gz (182967324 sequences in total) Writing a C -> T converted version of the input file trimmed_ACR-178-TP2_S1_R2_001.fastq.gz to trimmed_ACR-178-TP2_S1_R2_001.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file trimmed_ACR-178-TP2_S1_R2_001.fastq.gz to trimmed_ACR-178-TP2_S1_R2_001.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file trimmed_ACR-178-TP2_S1_R2_001.fastq.gz (182967324 sequences in total) Input files are trimmed_ACR-178-TP2_S1_R1_001.fastq.gz_C_to_T.fastq and trimmed_ACR-178-TP2_S1_R1_001.fastq.gz_G_to_A.fastq and trimmed_ACR-178-TP2_S1_R2_001.fastq.gz_C_to_T.fastq and trimmed_ACR-178-TP2_S1_R2_001.fastq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/data/ with the specified options: -q --score-min L,0,-1.0 -p 48 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from trimmed_ACR-178-TP2_S1_R1_001.fastq.gz_C_to_T.fastq and trimmed_ACR-178-TP2_S1_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.0 -p 48 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00260:131:22L7V3LT4:3:1101:3581:1014_1:N:0:GTCGGAGC+TNATAACC/1 77 * 0 0 * * 0 0 ANATAATTTTTTTTGTAAAATATTATATATTAAAATTTTAATTTAATTTTTAATAAAATATTATAAAAAATATAATATTTATTAAAAAATTATTAAAATTTATTAATTTTTTTAAAATAAATAATTTTTTTGAGT I#IIIII9IIII9IIII9IIIIII9I9IIIIIIIIIIIIIIIII9IIIIIII-IIIIIIIII9II9IIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIII-IIIIIIIII9IIIII9IIIIIII-I9IIIII9II YT:Z:UP LH00260:131:22L7V3LT4:3:1101:3581:1014_2:N:0:GTCGGAGC+TNATAACC/2 141 * 0 0 * * 0 0 ACTCAAAAAAATTATTTATTTTAAAAAAATTAATAAATTTTAATAATTTTTTCATAAATATTATATTTTTTATAATATTTTATTAAAAATTAAATTAAAATTTTAATATATAATATTTTAAAAAAAAAATTATTT IIIIIII99IIIIIIIIIIIIIIIIIIIIIII-II-III9IIIIII99II999II9-9III9999I9I-III-9-9999-99I-9-I-999III99--9-999I999II9I999I9-I99-9III-9II99III9 YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from trimmed_ACR-178-TP2_S1_R1_001.fastq.gz_G_to_A.fastq and trimmed_ACR-178-TP2_S1_R2_001.fastq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-1.0 -p 48 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00260:131:22L7V3LT4:3:1101:3581:1014_1:N:0:GTCGGAGC+TNATAACC/1 99 ptg000059l_GA_converted 1563633 1 130M1D5M = 1563869 372 ANACAACTTTTTCTACAAAATACCATACACTAAAATTTTAACCCAATTTTTAACAAAATATTACAAAAAATATAACATTTACTAAAAAACCACCAAAACTTATCAATCTCCTCAAAATAAACAACTTTTTTAAAT I#IIIII9IIII9IIII9IIIIII9I9IIIIIIIIIIIIIIIII9IIIIIII-IIIIIIIII9II9IIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIII-IIIIIIIII9IIIII9IIIIIII-I9IIIII9II AS:i:-21 XS:i:-21 XN:i:0 XM:i:3 XO:i:1 XG:i:1 NM:i:4 MD:Z:1A128^C2C1A0 YS:i:-32 YT:Z:CP LH00260:131:22L7V3LT4:3:1101:3581:1014_2:N:0:GTCGGAGC+TNATAACC/2 147 ptg000059l_GA_converted 1563869 1 130M1D5M = 1563633 -372 AAACAACTTTTTCTTCAAAATACCATACACTAAAATTTTAACCCAATTTTTAACAAAATATTACAAAAAATATAACATTTACAAAAAAACCACCAAAACTTATCAATCTCCTCAAAATAAACAACTTTTTTAAAT 9III99II9-III9-99I-9I999I9II999I999-9--99III999-I-9-I99-9999-9-III-I9I9999III9-9II999II99IIIIII9III-II-IIIIIIIIIIIIIIIIIIIIIII99IIIIIII AS:i:-32 XS:i:-38 XN:i:0 XM:i:4 XO:i:1 XG:i:1 NM:i:5 MD:Z:14A67T47^C2C1A0 YS:i:-21 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from trimmed_ACR-178-TP2_S1_R1_001.fastq.gz_G_to_A.fastq and trimmed_ACR-178-TP2_S1_R2_001.fastq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-1.0 -p 48 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00260:131:22L7V3LT4:3:1101:3581:1014_1:N:0:GTCGGAGC+TNATAACC/1 83 ptg000006l_CT_converted 3066 1 5M1D130M = 2830 -372 ATTTAAAAAAGTTGTTTATTTTGAGGAGATTGATAAGTTTTGGTGGTTTTTTAGTAAATGTTATATTTTTTGTAATATTTTGTTAAAAATTGGGTTAAAATTTTAGTGTATGGTATTTTGTAGAAAAAGTTGTNT II9IIIII9I-IIIIIII9IIIII9IIIIIIIII-IIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIII9II9IIIIIIIII-IIIIIII9IIIIIIIIIIIIIIIII9I9IIIIII9IIII9IIII9IIIII#I AS:i:-21 XS:i:-19 XN:i:0 XM:i:3 XO:i:1 XG:i:1 NM:i:4 MD:Z:0T1G2^G128T1 YS:i:-32 YT:Z:CP LH00260:131:22L7V3LT4:3:1101:3581:1014_2:N:0:GTCGGAGC+TNATAACC/2 163 ptg000006l_CT_converted 2830 1 5M1D130M = 3066 372 ATTTAAAAAAGTTGTTTATTTTGAGGAGATTGATAAGTTTTGGTGGTTTTTTTGTAAATGTTATATTTTTTGTAATATTTTGTTAAAAATTGGGTTAAAATTTTAGTGTATGGTATTTTGAAGAAAAAGTTGTTT IIIIIII99IIIIIIIIIIIIIIIIIIIIIII-II-III9IIIIII99II999II9-9III9999I9I-III-9-9999-99I-9-I-999III99--9-999I999II9I999I9-I99-9III-9II99III9 AS:i:-32 XS:i:-32 XN:i:0 XM:i:4 XO:i:1 XG:i:1 NM:i:5 MD:Z:0T1G2^G47A67T14 YS:i:-21 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from trimmed_ACR-178-TP2_S1_R1_001.fastq.gz_C_to_T.fastq and trimmed_ACR-178-TP2_S1_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.0 -p 48 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00260:131:22L7V3LT4:3:1101:3581:1014_1:N:0:GTCGGAGC+TNATAACC/1 77 * 0 0 * * 0 0 ANATAATTTTTTTTGTAAAATATTATATATTAAAATTTTAATTTAATTTTTAATAAAATATTATAAAAAATATAATATTTATTAAAAAATTATTAAAATTTATTAATTTTTTTAAAATAAATAATTTTTTTGAGT I#IIIII9IIII9IIII9IIIIII9I9IIIIIIIIIIIIIIIII9IIIIIII-IIIIIIIII9II9IIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIII-IIIIIIIII9IIIII9IIIIIII-I9IIIII9II YT:Z:UP LH00260:131:22L7V3LT4:3:1101:3581:1014_2:N:0:GTCGGAGC+TNATAACC/2 141 * 0 0 * * 0 0 ACTCAAAAAAATTATTTATTTTAAAAAAATTAATAAATTTTAATAATTTTTTCATAAATATTATATTTTTTATAATATTTTATTAAAAATTAAATTAAAATTTTAATATATAATATTTTAAAAAAAAAATTATTT IIIIIII99IIIIIIIIIIIIIIIIIIIIIII-II-III9IIIIII99II999II9-9III9999I9I-III-9-9999-99I-9-I-999III99--9-999I999II9I999I9-I99-9III-9II99III9 YT:Z:UP >>> Writing bisulfite mapping results to trimmed_ACR-178-TP2_S1_pe.bam <<< Reading in the sequence files ../output/01.00-D-Apul-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_ACR-178-TP2_S1_R1_001.fastq.gz and ../output/01.00-D-Apul-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_ACR-178-TP2_S1_R2_001.fastq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1117:30771:22278_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625590 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1119:13786:13523_1:N:0:GTCGGAGC+TTATAACC ptg000061l 2 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1120:29218:7486_1:N:0:GTCGGAGC+TTATAACC ptg000123l 44453 Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far 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 LH00260:131:22L7V3LT4:3:1143:43322:16381_1:N:0:GTCGGAGC+TTATAACC ptg000146l 1 Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1148:23294:12192_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625572 Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1149:15493:16451_1:N:0:GTCGGAGC+TTATAACC ptg000061l 250124 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 Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1177:11042:10371_1:N:0:GTCGGAGC+TTATAACC ptg000007l 12295874 Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1185:17905:24043_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625572 Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1193:33361:19308_1:N:0:GTCGGAGC+TTATAACC ptg000093l 1 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 LH00260:131:22L7V3LT4:3:1205:19240:6715_1:N:0:GTCGGAGC+TTATAACC ptg000039l 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1207:43832:11800_1:N:0:GTCGGAGC+TTATAACC ptg000093l 1 Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1211:39681:19406_1:N:0:GTCGGAGC+TTATAACC ptg000109l 39608 Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1217:26919:14209_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625591 Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1229:37035:23539_1:N:0:GTCGGAGC+TTATAACC ptg000122l 47625 Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1230:44739:14574_1:N:0:GTCGGAGC+TTATAACC ptg000152l 21001 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1231:26766:7948_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625572 Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1242:16068:14672_1:N:0:GTCGGAGC+TTATAACC ptg000056l 2 Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1245:6705:12977_1:N:0:GTCGGAGC+TTATAACC ptg000093l 1 Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1252:38580:1140_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625667 Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1257:7587:18706_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625572 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1257:7579:18720_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625572 Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1263:12491:9601_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625579 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1263:16545:23146_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625654 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1264:33822:12010_1:N:0:GTCGGAGC+TTATAACC ptg000093l 1 Processed 38000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1264:40110:23034_1:N:0:GTCGGAGC+TTATAACC ptg000109l 39583 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1265:29760:12066_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625624 Processed 39000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1268:15080:22460_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625625 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1269:3784:7696_1:N:0:GTCGGAGC+TTATAACC ptg000093l 1 Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1276:16796:4894_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625613 Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1282:17743:12725_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625629 Processed 43000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1288:8404:4516_1:N:0:GTCGGAGC+TTATAACC ptg000008l 38432908 Processed 44000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1292:21651:15344_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625572 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1292:21643:15358_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625572 Processed 45000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1295:6001:28063_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625632 Processed 46000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1296:17476:25990_1:N:0:GTCGGAGC+TTATAACC ptg000118l 34333 Processed 47000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1303:22363:24981_1:N:0:GTCAGAGC+TTATAACC ptg000122l 1 Processed 48000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1308:4561:2429_1:N:0:GTCGGAGC+TTATAACC ptg000117l 29997 Processed 49000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1311:28692:26522_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625584 Processed 50000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1317:48720:19364_1:N:0:GTCGGAGC+TTATAACC ptg000109l 39662 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1319:18018:28105_1:N:0:GTCGGAGC+TTATAACC ptg000146l 1 Processed 51000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1321:50856:29562_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625621 Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1331:7911:22796_1:N:0:GTCGGAGC+TTATAACC ptg000015l 14997081 Processed 54000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1338:23869:2429_1:N:0:GTCGGAGC+TTATAACC ptg000109l 39583 Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1344:33053:1378_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625631 Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1354:25252:13341_1:N:0:GTCGGAGC+TTATAACC ptg000090l 1 Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1359:41008:16885_1:N:0:GTCGGAGC+TTATAACC ptg000109l 39590 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1361:18528:28231_1:N:0:GTCGGAGC+TTATAACC ptg000045l 1 Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 63000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1374:12968:12080_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625572 Processed 64000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1378:50905:17375_1:N:0:GTCGGAGC+TTATAACC ptg000090l 1 Processed 65000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1380:28578:20135_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625627 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1383:14223:4390_1:N:0:GTCGGAGC+TTATAACC ptg000174l 27214 Processed 66000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1384:33142:11926_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625658 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1384:14037:14069_1:N:0:GTCGGAGC+TTATAACC ptg000122l 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1385:50654:21675_1:N:0:GTCGGAGC+TTATAACC ptg000127l 27792 Processed 67000000 sequence pairs so far Processed 68000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1393:32503:27545_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625625 Processed 69000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1396:13260:8382_1:N:0:GTCGGAGC+TTATAACC ptg000122l 1 Processed 70000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1403:34842:23216_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625593 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1407:33596:2737_1:N:0:GTCGGAGC+TTATAACC ptg000007l 12295881 Processed 71000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1407:28190:7920_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625629 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1407:9246:22362_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625584 Processed 72000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1411:30067:18426_1:N:0:GTCGGAGC+TTATAACC ptg000027l 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1413:37277:24687_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625590 Processed 73000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1418:50800:6043_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625572 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1418:14724:8060_1:N:0:GTCGGAGC+TTATAACC ptg000061l 1 Processed 74000000 sequence pairs so far Processed 75000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1426:42837:8032_1:N:0:GTCGGAGC+TTATAACC ptg000093l 1 Processed 76000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1429:39033:22096_1:N:0:GTCGGAGC+TTATAACC ptg000061l 2 Processed 77000000 sequence pairs so far Processed 78000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1440:6721:7794_1:N:0:GTCGGAGC+TTATAACC ptg000174l 27214 Processed 79000000 sequence pairs so far Processed 80000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1448:49537:11534_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625625 Processed 81000000 sequence pairs so far Processed 82000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1454:26466:19000_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625615 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1455:27939:26088_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625628 Processed 83000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1458:39988:1840_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625658 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1459:25965:29086_1:N:0:GTCGGAGC+TTATAACC ptg000015l 14997064 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1461:19636:14742_1:N:0:GTCGGAGC+TTATAACC ptg000125l 18853 Processed 84000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1465:49861:7219_1:N:0:GTCGGAGC+TTATAACC ptg000093l 1 Processed 85000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1468:49618:12206_1:N:0:GTCGGAGC+TTATAACC ptg000146l 3 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1469:35967:4096_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625628 Processed 86000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1473:31095:27012_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625572 Processed 87000000 sequence pairs so far Processed 88000000 sequence pairs so far Processed 89000000 sequence pairs so far Processed 90000000 sequence pairs so far Processed 91000000 sequence pairs so far Processed 92000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1495:21239:15162_1:N:0:GTCGGAGC+TTATAACC ptg000127l 27810 Processed 93000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1497:28732:27461_1:N:0:GTCGGAGC+TTATAACC ptg000006l 2 Processed 94000000 sequence pairs so far Processed 95000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2111:17201:10469_1:N:0:GTCGGAGC+TTATAACC ptg000093l 1 Processed 96000000 sequence pairs so far Processed 97000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2123:42537:26088_1:N:0:GTCGGAGC+TTATAACC ptg000061l 250129 Processed 98000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2128:2756:5440_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625612 Processed 99000000 sequence pairs so far Processed 100000000 sequence pairs so far Processed 101000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2141:39470:15372_1:N:0:GTCGGAGC+TTATAACC ptg000122l 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2141:39487:15372_1:N:0:GTCGGAGC+TTATAACC ptg000122l 1 Processed 102000000 sequence pairs so far Processed 103000000 sequence pairs so far Processed 104000000 sequence pairs so far Processed 105000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2158:44868:2975_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625581 Processed 106000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2162:48194:9909_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625572 Processed 107000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2163:7692:28553_1:N:0:GTCGGAGC+TTATAACC ptg000090l 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2165:28934:26074_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625616 Processed 108000000 sequence pairs so far Processed 109000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2174:13203:27783_1:N:0:GTCGGAGC+TTATAACC ptg000069l 259811 Processed 110000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2175:24856:5006_1:N:0:GTCGGAGC+TTATAACC ptg000056l 1 Processed 111000000 sequence pairs so far Processed 112000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2186:27211:5833_1:N:0:GTCGGAGC+TTATAACC ptg000146l 2 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2186:27219:5847_1:N:0:GTCGGAGC+TTATAACC ptg000146l 2 Processed 113000000 sequence pairs so far Processed 114000000 sequence pairs so far Processed 115000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2195:7878:17081_1:N:0:GTCGGAGC+TTATAACC ptg000130l 1 Processed 116000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2203:15615:28119_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625666 Processed 117000000 sequence pairs so far Processed 118000000 sequence pairs so far Processed 119000000 sequence pairs so far Processed 120000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2220:34874:12711_1:N:0:ATCGGAGC+TTATAACC ptg000082l 2 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2222:4633:27853_1:N:0:GTCGGAGC+TTATAACC ptg000153l 25739 Processed 121000000 sequence pairs so far Processed 122000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2228:11382:18356_1:N:0:GTCGGAGC+TTATAACC ptg000146l 1 Processed 123000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2234:20462:4432_1:N:0:GTCGGAGC+TTATAACC ptg000093l 1 Processed 124000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2237:36315:19322_1:N:0:GTCGGAGC+TTATAACC ptg000117l 30013 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2238:46211:17235_1:N:0:GTCGGAGC+TTATAACC ptg000025l 21443060 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2239:28052:25920_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625600 Processed 125000000 sequence pairs so far Processed 126000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2248:34308:1364_1:N:0:GTCGGAGC+TTATCACC ptg000033l 2625629 Processed 127000000 sequence pairs so far Processed 128000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2257:13235:10441_1:N:0:GTCGGAGC+TTATAACC ptg000109l 39605 Processed 129000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2262:38208:19238_1:N:0:GTCGGAGC+TTATAACC ptg000007l 12295841 Processed 130000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2266:11318:27349_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625637 Processed 131000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2270:26766:16325_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625590 Processed 132000000 sequence pairs so far Processed 133000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2277:13066:16815_1:N:0:GTCGGAGC+TTATAACC ptg000146l 2 Processed 134000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2281:41040:25878_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625615 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2281:41057:25878_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625615 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2281:41032:25892_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625615 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2281:41048:25892_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625615 Processed 135000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2285:46567:9251_1:N:0:GTCGGAGC+TTATAACC ptg000030l 2 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2285:13235:14588_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625627 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2287:3339:13285_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625658 Processed 136000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2289:29161:8424_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625570 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2289:51139:8760_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625570 Processed 137000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2297:42198:7261_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625577 Processed 138000000 sequence pairs so far Processed 139000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2309:45604:16605_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625577 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2309:6001:29436_1:N:0:ATCGGAGC+TTATAACC ptg000033l 2625688 Processed 140000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2311:17913:6715_1:N:0:GTCGGAGC+TTATAACC ptg000093l 1 Processed 141000000 sequence pairs so far Processed 142000000 sequence pairs so far Processed 143000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2325:51431:3465_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625628 Processed 144000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2330:38977:14938_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625573 Processed 145000000 sequence pairs so far Processed 146000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2339:27923:4852_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625572 Processed 147000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2344:12289:26116_1:N:0:GTCGGAGC+TTATAACC ptg000109l 39606 Processed 148000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2348:14166:8830_1:N:0:GTCGGAGC+TTATAACC ptg000092l 1 Processed 149000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2350:48251:24379_1:N:0:ATCGGAGC+TTATAACC ptg000033l 2625572 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2351:8032:27657_1:N:0:GTCGGAGC+TTATAACC ptg000128l 1 Processed 150000000 sequence pairs so far Processed 151000000 sequence pairs so far Processed 152000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2366:44140:3059_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625624 Processed 153000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2368:22687:16997_1:N:0:GTCGGAGC+TTATAACC ptg000069l 259768 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2368:22695:17011_1:N:0:GTCGGAGC+TTATAACC ptg000069l 259768 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2369:51423:3844_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625572 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2369:50767:19546_1:N:0:GTCGGAGC+TTATAACC ptg000109l 39590 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2370:27494:9825_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625572 Processed 154000000 sequence pairs so far Processed 155000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2376:9675:27307_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625624 Processed 156000000 sequence pairs so far Processed 157000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2387:46486:27405_1:N:0:GTCGGAGC+TTATAACC ptg000018l 3 Processed 158000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2392:41453:4012_1:N:0:GTCGGAGC+TTATAACC ptg000109l 39589 Processed 159000000 sequence pairs so far Processed 160000000 sequence pairs so far Processed 161000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2407:10638:15610_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625665 Processed 162000000 sequence pairs so far Processed 163000000 sequence pairs so far Processed 164000000 sequence pairs so far Processed 165000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2427:14603:13061_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625589 Processed 166000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2432:38710:13719_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625609 Processed 167000000 sequence pairs so far 182967324 reads; of these: 182967324 (100.00%) were paired; of these: 137379430 (75.08%) aligned concordantly 0 times 14799364 (8.09%) aligned concordantly exactly 1 time 30788530 (16.83%) aligned concordantly >1 times 24.92% overall alignment rate Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2436:4059:22880_1:N:0:GTCGGAGC+TTATAACC ptg000109l 39659 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2437:4577:20639_1:N:0:GTCGGAGC+TTATAACC ptg000061l 1 Processed 168000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2440:40053:25149_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625571 Processed 169000000 sequence pairs so far 182967324 reads; of these: 182967324 (100.00%) were paired; of these: 122405770 (66.90%) aligned concordantly 0 times 19413525 (10.61%) aligned concordantly exactly 1 time 41148029 (22.49%) aligned concordantly >1 times 33.10% overall alignment rate Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2446:50589:13075_1:N:0:GTCGGAGC+TTATAACC ptg000109l 39607 Processed 170000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2449:44828:7444_1:N:0:GTCGGAGC+TTATAACC ptg000074l 12210 Processed 171000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2453:34801:14237_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625634 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2453:50233:25037_1:N:0:GTCGGAGC+TTATAACC ptg000109l 39607 Processed 172000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2457:47652:14882_1:N:0:GTCGGAGC+TTATAACC ptg000069l 259768 Processed 173000000 sequence pairs so far 182967324 reads; of these: 182967324 (100.00%) were paired; of these: 137414901 (75.10%) aligned concordantly 0 times 14786659 (8.08%) aligned concordantly exactly 1 time 30765764 (16.81%) aligned concordantly >1 times 24.90% overall alignment rate Processed 174000000 sequence pairs so far Processed 175000000 sequence pairs so far 182967324 reads; of these: 182967324 (100.00%) were paired; of these: 122402919 (66.90%) aligned concordantly 0 times 19439080 (10.62%) aligned concordantly exactly 1 time 41125325 (22.48%) aligned concordantly >1 times 33.10% overall alignment rate Processed 176000000 sequence pairs so far Processed 177000000 sequence pairs so far Processed 178000000 sequence pairs so far Processed 179000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2485:44285:29310_1:N:0:GTCGGAGC+TTATAACC ptg000026l 1 Processed 180000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2486:17638:8956_1:N:0:GTCGGAGC+TTATAACC ptg000122l 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2487:13260:14630_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625577 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2487:37998:14812_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625667 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2488:16828:4782_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625613 Processed 181000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2490:30132:19630_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625575 Processed 182000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2495:47101:19056_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625575 Processed 182967324 sequences in total Successfully deleted the temporary files trimmed_ACR-178-TP2_S1_R1_001.fastq.gz_C_to_T.fastq, trimmed_ACR-178-TP2_S1_R1_001.fastq.gz_G_to_A.fastq, trimmed_ACR-178-TP2_S1_R2_001.fastq.gz_C_to_T.fastq and trimmed_ACR-178-TP2_S1_R2_001.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 182967324 Final Cytosine Methylation Report ================================= Total number of C's analysed: 3994751719 Total methylated C's in CpG context: 70399594 Total methylated C's in CHG context: 12957412 Total methylated C's in CHH context: 62458470 Total methylated C's in Unknown context: 11680962 Total unmethylated C's in CpG context: 629501595 Total unmethylated C's in CHG context: 739934104 Total unmethylated C's in CHH context: 2479500544 Total unmethylated C's in Unknown context: 43368441 C methylated in CpG context: 10.1% C methylated in CHG context: 1.7% C methylated in CHH context: 2.5% C methylated in unknown context (CN or CHN): 21.2% Bismark completed in 1d 1h 6m 22s ==================== Bismark run complete ====================