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 8 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-145-TP2_S3_R1_001.fastq.gz ../output/01.00-D-Apul-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_ACR-145-TP2_S3_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 8 --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-145-TP2_S3_R1_001.fastq.gz and ../output/01.00-D-Apul-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_ACR-145-TP2_S3_R2_001.fastq.gz Input files are in FastQ format Writing a C -> T converted version of the input file trimmed_ACR-145-TP2_S3_R1_001.fastq.gz to trimmed_ACR-145-TP2_S3_R1_001.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file trimmed_ACR-145-TP2_S3_R1_001.fastq.gz to trimmed_ACR-145-TP2_S3_R1_001.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file trimmed_ACR-145-TP2_S3_R1_001.fastq.gz (244866108 sequences in total) Writing a C -> T converted version of the input file trimmed_ACR-145-TP2_S3_R2_001.fastq.gz to trimmed_ACR-145-TP2_S3_R2_001.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file trimmed_ACR-145-TP2_S3_R2_001.fastq.gz to trimmed_ACR-145-TP2_S3_R2_001.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file trimmed_ACR-145-TP2_S3_R2_001.fastq.gz (244866108 sequences in total) Input files are trimmed_ACR-145-TP2_S3_R1_001.fastq.gz_C_to_T.fastq and trimmed_ACR-145-TP2_S3_R1_001.fastq.gz_G_to_A.fastq and trimmed_ACR-145-TP2_S3_R2_001.fastq.gz_C_to_T.fastq and trimmed_ACR-145-TP2_S3_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 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 trimmed_ACR-145-TP2_S3_R1_001.fastq.gz_C_to_T.fastq and trimmed_ACR-145-TP2_S3_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.0 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00260:131:22L7V3LT4:3:1101:1397:1014_1:N:0:TTACAGGA+GNTTGTCA/1 77 * 0 0 * * 0 0 TNATAATGTAATTTTATGTATGTATATATAATTTATTTGTGGTGTGAAGAGGTTGAAATTTTTTAGTTTTTGTTGATAAATTAATTTAATT I#IIIIII9IIIIII-IIIIIIIIIII9II--II-IIII99IIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIII-9II-IIIIIIII YT:Z:UP LH00260:131:22L7V3LT4:3:1101:1397:1014_2:N:0:TTACAGGA+GNTTGTCA/2 141 * 0 0 * * 0 0 AATTAAATTAATTTATCAACAAAAACTAAAAAATTTCAACCTCTTCACACCACAAATAAATTATATATACATACATAAAATTACATTATAA I9IIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIII9-9IIII-I-IIIII-I9IIIII9IIIIII9I99999IIII9 YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from trimmed_ACR-145-TP2_S3_R1_001.fastq.gz_G_to_A.fastq and trimmed_ACR-145-TP2_S3_R2_001.fastq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-1.0 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00260:131:22L7V3LT4:3:1101:1397:1014_1:N:0:TTACAGGA+GNTTGTCA/1 77 * 0 0 * * 0 0 CNACAATATAATTTTATATATATATATATAATTTATTTATAATATAAAAAAATTAAAATTTTTTAATTTTTATTAATAAATTAATTTAATT I#IIIIII9IIIIII-IIIIIIIIIII9II--II-IIII99IIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIII-9II-IIIIIIII YT:Z:UP LH00260:131:22L7V3LT4:3:1101:1397:1014_2:N:0:TTACAGGA+GNTTGTCA/2 141 * 0 0 * * 0 0 AATTAAATTAATTTATTAATAAAAATTAAAAAATTTTAATTTTTTTATATTATAAATAAATTATATATATATATATAAAATTATATTGTGG I9IIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIII9-9IIII-I-IIIII-I9IIIII9IIIIII9I99999IIII9 YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from trimmed_ACR-145-TP2_S3_R1_001.fastq.gz_G_to_A.fastq and trimmed_ACR-145-TP2_S3_R2_001.fastq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-1.0 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00260:131:22L7V3LT4:3:1101:1397:1014_1:N:0:TTACAGGA+GNTTGTCA/1 77 * 0 0 * * 0 0 CNACAATATAATTTTATATATATATATATAATTTATTTATAATATAAAAAAATTAAAATTTTTTAATTTTTATTAATAAATTAATTTAATT I#IIIIII9IIIIII-IIIIIIIIIII9II--II-IIII99IIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIII-9II-IIIIIIII YT:Z:UP LH00260:131:22L7V3LT4:3:1101:1397:1014_2:N:0:TTACAGGA+GNTTGTCA/2 141 * 0 0 * * 0 0 AATTAAATTAATTTATTAATAAAAATTAAAAAATTTTAATTTTTTTATATTATAAATAAATTATATATATATATATAAAATTATATTGTGG I9IIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIII9-9IIII-I-IIIII-I9IIIII9IIIIII9I99999IIII9 YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from trimmed_ACR-145-TP2_S3_R1_001.fastq.gz_C_to_T.fastq and trimmed_ACR-145-TP2_S3_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.0 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00260:131:22L7V3LT4:3:1101:1397:1014_1:N:0:TTACAGGA+GNTTGTCA/1 83 ntLink_8_GA_converted 18071658 4 87M2D4M = 18071658 -93 AATTAAATTAATTTATCAACAAAAACTAAAAAATTTCAACCTCTTCACACCACAAATAAATTATATATACATACATAAAATTACATTATNA IIIIIIII-II9-IIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIII99IIII-II--II9IIIIIIIIIII-IIIIII9IIIIII#I AS:i:-42 XS:i:-88 XN:i:0 XM:i:6 XO:i:1 XG:i:2 NM:i:8 MD:Z:36T2A11C4C21T8^CC2C1 YS:i:-47 YT:Z:CP LH00260:131:22L7V3LT4:3:1101:1397:1014_2:N:0:TTACAGGA+GNTTGTCA/2 163 ntLink_8_GA_converted 18071658 4 87M2D4M = 18071658 93 AATTAAATTAATTTATCAACAAAAACTAAAAAATTTCAACCTCTTCACACCACAAATAAATTATATATACATACATAAAATTACATTATAA I9IIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIII9-9IIII-I-IIIII-I9IIIII9IIIIII9I99999IIII9 AS:i:-47 XS:i:-87 XN:i:0 XM:i:6 XO:i:1 XG:i:2 NM:i:8 MD:Z:36T2A11C4C21T8^CC2C1 YS:i:-42 YT:Z:CP >>> Writing bisulfite mapping results to trimmed_ACR-145-TP2_S3_pe.bam <<< Reading in the sequence files ../output/01.00-D-Apul-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_ACR-145-TP2_S3_R1_001.fastq.gz and ../output/01.00-D-Apul-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_ACR-145-TP2_S3_R2_001.fastq.gz Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1101:8412:27195_1:N:0:TTACAGGA+GCTAGTCA ptg000105l 1 Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far 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 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 LH00260:131:22L7V3LT4:3:1143:4140:19070_1:N:0:TTACAGGA+GCTTGTCA ptg000093l 1 Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1147:49683:8452_1:N:0:TTACAGGA+GCTTGTCA ptg000109l 39608 Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1148:10322:15988_1:N:0:TTACAGGA+GCTTGTCA ptg000082l 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1149:47433:12626_1:N:0:TTACAGGA+GCTTGTCA ptg000007l 12295844 Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1151:19264:27153_1:N:0:TTACAGGA+GCTTGTCA ptg000109l 39608 Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1154:9117:27685_1:N:0:TTACAGGA+GATTGTCA ptg000093l 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1155:44601:16773_1:N:0:TTACAGGA+GCTTGTCA ptg000082l 1 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 LH00260:131:22L7V3LT4:3:1165:25439:14980_1:N:0:TTACAGGA+GCTTGTCA ptg000090l 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1166:31750:20583_1:N:0:TTACAGGA+GCTTGTCA ptg000093l 1 Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1170:21142:11128_1:N:0:TTACAGGA+GCTTGTCA ptg000033l 2625615 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1170:21150:11142_1:N:0:TTACAGGA+GCTTGTCA ptg000033l 2625615 Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far 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 LH00260:131:22L7V3LT4:3:1190:28837:10609_1:N:0:TTACAGGA+GCTTGTCA ptg000066l 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1190:28821:10637_1:N:0:TTACAGGA+GCTTGTCC ptg000066l 1 Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1201:6025:7346_1:N:0:TCACAGGA+GCTTGTCA ptg000024l 12381238 Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1206:42092:14644_1:N:0:TTACAGGA+GCTTGTCA ptg000033l 2625649 Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1215:46843:14798_1:N:0:TTACAGGA+GCTTGTCA ptg000090l 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 LH00260:131:22L7V3LT4:3:1226:3403:13817_1:N:0:TTACAGGA+GCTTGTCA ptg000133l 37086 Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1234:20721:18944_1:N:0:TTACAGGA+GCTTGTCA ptg000117l 29997 Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1245:31427:18622_1:N:0:TTACAGGA+GCTTGTCA ptg000015l 14997081 Processed 45000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1249:31920:10651_1:N:0:TTACAGGA+GCTTGTCA ptg000074l 12211 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1249:47304:18174_1:N:0:TTACAGGA+GCTTGTCA ptg000033l 2625572 Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1261:52119:18300_1:N:0:TTACAGGA+GCTTGTCA ptg000093l 1 Processed 50000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1264:6875:14167_1:N:0:TTACAGGA+GCTTGTCA ptg000090l 1 Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1271:33434:26522_1:N:0:TTACAGGA+GCTTGTCA ptg000088l 96868 Processed 53000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1272:2707:28833_1:N:0:TTACAGGA+GCTTGTCA ptg000090l 1 Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1279:30108:17879_1:N:0:TTACAGGA+GCTTGTCA ptg000140l 1 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 LH00260:131:22L7V3LT4:3:1297:17832:21059_1:N:0:TTACAGGA+GCTTGTCA ptg000113l 2 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1297:17824:21073_1:N:0:TTACAGGA+GCTTGTCA ptg000113l 2 Processed 62000000 sequence pairs so far Processed 63000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1305:45426:14447_1:N:0:TTACAGGA+GCTTGTCA ptg000117l 29997 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1306:37318:6939_1:N:0:TTACAGGA+GCTTGTCA ptg000090l 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 Processed 69000000 sequence pairs so far Processed 70000000 sequence pairs so far Processed 71000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1331:12054:11282_1:N:0:TTACAGGA+GCTTGTCA ptg000095l 2 Processed 72000000 sequence pairs so far Processed 73000000 sequence pairs so far Processed 74000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1342:51164:10175_1:N:0:TTACAGGA+GCTTGTCA ptg000146l 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1342:47822:25990_1:N:0:TTACAGGA+GCTTGTCA ptg000122l 1 Processed 75000000 sequence pairs so far Processed 76000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1347:32098:28245_1:N:0:TTACAGGA+GCTTGTCA ptg000033l 2625593 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1348:12224:14994_1:N:0:TTACAGGA+GCTTGTCA ptg000033l 2625571 Processed 77000000 sequence pairs so far Processed 78000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1354:20494:13425_1:N:0:TTACAGGA+GCTTGTCA ptg000061l 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1355:11649:12795_1:N:0:TTACAGGA+GCTGGTCA ptg000069l 259796 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1355:8315:18706_1:N:0:TTACAGGA+GCTTGTCA ptg000109l 39608 Processed 79000000 sequence pairs so far Processed 80000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1362:33393:3199_1:N:0:TTACAGGA+GCTTGTCA ptg000007l 12295858 Processed 81000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1365:48906:15960_1:N:0:TTACAGGA+GCTTGTCA ptg000117l 29978 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1365:48906:15988_1:N:0:TTACAGGA+GCTTGTCA ptg000117l 29978 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1365:48922:15988_1:N:0:TTACAGGA+GCTTGTCA ptg000117l 29978 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1365:48938:15988_1:N:0:TTACAGGA+GCTTGTCA ptg000160l 32567 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1365:48914:16002_1:N:0:TTACAGGA+GCTTGTCA ptg000160l 32567 Processed 82000000 sequence pairs so far Processed 83000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1370:2748:3045_1:N:0:TTACAGGA+GCTTGTCA ptg000113l 1 Processed 84000000 sequence pairs so far Processed 85000000 sequence pairs so far Processed 86000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1380:40425:4698_1:N:0:TTACAGGA+GCTTGTCA ptg000123l 1 Processed 87000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1380:17314:25738_1:N:0:TTACAGGA+GCTTGTCA ptg000061l 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1383:14813:2751_1:N:0:TTACAGGA+GCTTGTCA ptg000033l 2625658 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 Processed 93000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1402:8396:16240_1:N:0:TTACAGGA+GCTTGTCA ptg000004l 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1402:8412:16240_1:N:0:TTACAGGA+GCTTGTCA ptg000004l 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1403:48631:16913_1:N:0:TTACAGGA+GCTTGTCA ptg000033l 2625658 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1403:37553:29394_1:N:0:TTACAGGA+GCTTGTCA ptg000093l 1 Processed 94000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1405:46041:23833_1:N:0:TTACAGGA+GCTTGTCA ptg000033l 2625649 Processed 95000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1410:38969:10497_1:N:0:TTACAGGA+GCTTGTCA ptg000033l 2625624 Processed 96000000 sequence pairs so far Processed 97000000 sequence pairs so far Processed 98000000 sequence pairs so far Processed 99000000 sequence pairs so far Processed 100000000 sequence pairs so far Processed 101000000 sequence pairs so far Processed 102000000 sequence pairs so far Processed 103000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1433:10864:26228_1:N:0:TTACAGGA+GCTTGTCA ntLink_1 163090 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1433:40223:28889_1:N:0:TTACAGGA+GCTTGTCA ptg000118l 34353 Processed 104000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1437:13001:12753_1:N:0:TTACAGGA+GCTTGTCA ptg000125l 18910 Processed 105000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1441:18220:16325_1:N:0:TTACAGGA+GCTTGTCA ptg000093l 1 Processed 106000000 sequence pairs so far Processed 107000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1446:4698:23370_1:N:0:TTACAGGA+GCTTGTCA ptg000088l 96868 Processed 108000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1449:8453:22978_1:N:0:TTACAGGA+GCTTGTCA ptg000033l 2625658 Processed 109000000 sequence pairs so far Processed 110000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1457:35141:2051_1:N:0:TTACAGGA+GCTTGTCA ptg000090l 1 Processed 111000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1460:46025:18398_1:N:0:TTACAGGA+GCTTGTCA ptg000082l 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1461:42683:25107_1:N:0:TTACAGGA+GCTTGTCA ptg000093l 1 Processed 112000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1462:18803:3577_1:N:0:TTACAGGA+GCTTGTCA ptg000109l 39608 Processed 113000000 sequence pairs so far Processed 114000000 sequence pairs so far Processed 115000000 sequence pairs so far Processed 116000000 sequence pairs so far 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 LH00260:131:22L7V3LT4:3:1485:19580:24505_1:N:0:TTACAGGA+GCTTGTCA ptg000066l 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1486:39446:17011_1:N:0:TTACAGGA+GCTTGTCA ptg000109l 39608 Processed 121000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1491:24993:1546_1:N:0:TTACAGGA+GCTTGTCA ptg000033l 2625572 Processed 122000000 sequence pairs so far Processed 123000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1494:15453:20835_1:N:0:TTACAGGA+GCTTGTCA ptg000033l 2625575 Processed 124000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1498:29185:19981_1:N:0:TTACAGGA+ACTTGTCA ptg000023l 1 Processed 125000000 sequence pairs so far Processed 126000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2106:49958:12991_1:N:0:TTACAGGA+GCTTGTCA ptg000090l 1 Processed 127000000 sequence pairs so far Processed 128000000 sequence pairs so far Processed 129000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2120:19717:4068_1:N:0:TTACAGGA+GCTTGTCA ptg000033l 2625624 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2120:19709:4082_1:N:0:TTACAGGA+GCTTGTCA ptg000033l 2625624 Processed 130000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2124:42804:18930_1:N:0:TTACAGGA+GCTCGTCA ptg000033l 2625649 Processed 131000000 sequence pairs so far Processed 132000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2128:41089:27587_1:N:0:TTACAGGA+GCTTGTCA ptg000122l 1 Processed 133000000 sequence pairs so far Processed 134000000 sequence pairs so far Processed 135000000 sequence pairs so far Processed 136000000 sequence pairs so far Processed 137000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2148:26879:21087_1:N:0:TTACAGGA+GCTTGTCA ptg000061l 1 Processed 138000000 sequence pairs so far Processed 139000000 sequence pairs so far Processed 140000000 sequence pairs so far Processed 141000000 sequence pairs so far Processed 142000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2162:30561:14041_1:N:0:TTACAGGA+GCTTGTCA ptg000109l 39608 Processed 143000000 sequence pairs so far Processed 144000000 sequence pairs so far Processed 145000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2171:35206:16170_1:N:0:TTACAGGA+GCTTGTCA ptg000033l 2625572 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2171:35198:16184_1:N:0:TTACAGGA+GCTTGTCA ptg000033l 2625572 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2171:35206:16198_1:N:0:TTACAGGA+GCTTGTCA ptg000033l 2625572 Processed 146000000 sequence pairs so far Processed 147000000 sequence pairs so far Processed 148000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2179:5596:13271_1:N:0:TTACAGGA+GCTTGTCA ptg000090l 49452 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2180:25244:20723_1:N:0:TTACAGGA+GCTTGTCA ptg000033l 2625658 Processed 149000000 sequence pairs so far Processed 150000000 sequence pairs so far Processed 151000000 sequence pairs so far Processed 152000000 sequence pairs so far Processed 153000000 sequence pairs so far Processed 154000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2195:38855:17529_1:N:0:TTACAGGA+GCGTGTCA ptg000082l 1 Processed 155000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2198:33458:17907_1:N:0:TTACAGGA+GCTTGTCA ptg000033l 2625652 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2201:24354:26242_1:N:0:TTACAGGA+GCTTGTCA ptg000135l 25300 Processed 156000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2203:49715:8396_1:N:0:TTACAGGA+GCTTGTCA ptg000069l 259792 Processed 157000000 sequence pairs so far Processed 158000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2210:29072:15218_1:N:0:TTACAGGA+GCTTGTCA ptg000056l 1 Processed 159000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2214:42829:24491_1:N:0:TTACAGGA+GCTTGTCA ptg000033l 2625658 Processed 160000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2220:29088:22418_1:N:0:TTACAGGA+GCTTGTCA ptg000033l 2625658 Processed 161000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2222:6187:9335_1:N:0:TTACAGGA+GCTTGTCA ptg000033l 2625620 Processed 162000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2225:6616:5707_1:N:0:TTACAGGA+GCTTGTCA ptg000033l 2625655 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2227:31597:17991_1:N:0:TTACAGGA+GCTTGTCA ptg000033l 2625572 Processed 163000000 sequence pairs so far Processed 164000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2232:4617:18664_1:N:0:TTACAGGA+GCTTGTCA ptg000093l 1 Processed 165000000 sequence pairs so far Processed 166000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2240:19450:6155_1:N:0:TTACAGGA+GCTTGTCA ptg000018l 16820849 Processed 167000000 sequence pairs so far Processed 168000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2245:49780:9012_1:N:0:TTACAGGA+GCTTGTCA ptg000033l 2625658 Processed 169000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2250:14902:20555_1:N:0:TTACAGGA+GCTTGTCA ptg000122l 1 Processed 170000000 sequence pairs so far Processed 171000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2255:51131:1518_1:N:0:TTACAGGA+GCTTGTCA ptg000033l 2625649 Processed 172000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2258:41704:14756_1:N:0:TTACAGGA+GCTTGTCA ptg000090l 1 Processed 173000000 sequence pairs so far Processed 174000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2266:50274:22586_1:N:0:TTACAGGA+GCTTGTCA ptg000090l 1 Processed 175000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2270:17735:3381_1:N:0:TTACAGGA+GCTTGTCA ptg000033l 2625589 Processed 176000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2271:13284:4894_1:N:0:TTACAGGA+GCTTGTCA ptg000093l 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2272:25851:8130_1:N:0:TTACAGGA+GCTTGTCA ptg000033l 2625624 Processed 177000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2273:19547:8200_1:N:0:TTACAGGA+GCTTGTCA ptg000095l 40202 Processed 178000000 sequence pairs so far Processed 179000000 sequence pairs so far Processed 180000000 sequence pairs so far Processed 181000000 sequence pairs so far Processed 182000000 sequence pairs so far Processed 183000000 sequence pairs so far Processed 184000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2296:40029:9447_1:N:0:TTACAGGA+GCTTGTCA ptg000061l 1 Processed 185000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2304:21611:23679_1:N:0:TTACAGGA+GCTTGTCA ptg000093l 1 Processed 186000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2308:40555:12739_1:N:0:TTACAGGA+GCTTGTCA ptg000033l 2625649 Processed 187000000 sequence pairs so far Processed 188000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2313:28813:9475_1:N:0:TTACAGGA+GCTTGTCA ptg000033l 2625580 Processed 189000000 sequence pairs so far Processed 190000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2320:10452:24365_1:N:0:TTACAGGA+GCTTGTCA ptg000007l 12295858 Processed 191000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2323:24896:18216_1:N:0:TTACAGGA+ACTTGTCA ptg000061l 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2325:11075:22754_1:N:0:TTACAGGA+GCTTGTCA ptg000122l 1 Processed 192000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2328:32333:17697_1:N:0:TTACAGGA+GCTTGTCA ptg000056l 1 Processed 193000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2330:47207:22712_1:N:0:TTACAGGA+GCTTGTCA ptg000033l 2625649 Processed 194000000 sequence pairs so far Processed 195000000 sequence pairs so far Processed 196000000 sequence pairs so far Processed 197000000 sequence pairs so far Processed 198000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2348:8445:7275_1:N:0:TTACAGGA+GCTTGTCA ptg000015l 14997066 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2348:48801:21605_1:N:0:TTACAGGA+GCTTGTCA ptg000036l 6407180 Processed 199000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2352:3711:8802_1:N:0:TTACAGGA+ACTTGTCA ptg000146l 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2352:3727:8802_1:N:0:TTACAGGA+ACTTGTCA ptg000146l 1 Processed 200000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2355:51390:14153_1:N:0:TTACAGGA+GCTTGTCA ptg000033l 2625649 Processed 201000000 sequence pairs so far Processed 202000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2360:51787:28455_1:N:0:TTACAGGA+GCTTGTCA ptg000035l 10246561 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2361:10848:3872_1:N:0:TTACAGGA+GCTTGTCA ptg000095l 40213 Processed 203000000 sequence pairs so far Processed 204000000 sequence pairs so far Processed 205000000 sequence pairs so far Processed 206000000 sequence pairs so far Processed 207000000 sequence pairs so far Processed 208000000 sequence pairs so far Processed 209000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2382:39624:19056_1:N:0:TTACAGGA+GCTTGTCA ptg000093l 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2383:35295:14307_1:N:0:TTACAGGA+GCTTGTCA ptg000065l 2 Processed 210000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2384:49998:18944_1:N:0:TTACAGGA+GCTTGTCA ptg000140l 1 Processed 211000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2388:11164:23244_1:N:0:TTACAGGA+ACTTGTCA ptg000154l 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2390:44107:10988_1:N:0:TTACAGGA+GCTTGTCA ptg000056l 1 Processed 212000000 sequence pairs so far Processed 213000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2395:17524:28960_1:N:0:TTACAGGA+GCTTGTCA ptg000144l 1 Processed 214000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2398:39001:28988_1:N:0:TTACAGGA+GCTTGTCA ptg000033l 2625580 Processed 215000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2404:18382:29296_1:N:0:TTACAGGA+GCTTGTCA ptg000088l 96868 Processed 216000000 sequence pairs so far Processed 217000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2410:32082:28273_1:N:0:TTACAGGA+GCTTGTCA ptg000093l 1 Processed 218000000 sequence pairs so far Processed 219000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2419:23051:28749_1:N:0:TTACAGGA+GCTTGTCA ptg000008l 38432907 Processed 220000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2423:8688:22516_1:N:0:TTACAGGA+GCTTGTCA ptg000025l 21443056 Processed 221000000 sequence pairs so far Processed 222000000 sequence pairs so far Processed 223000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2433:9942:16479_1:N:0:TTACAGGA+GCTTGTCA ptg000109l 39658 Processed 224000000 sequence pairs so far Processed 225000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2441:20680:22628_1:N:0:TTACAGGA+GCTTGTCA ptg000023l 3 Processed 226000000 sequence pairs so far Processed 227000000 sequence pairs so far 244866108 reads; of these: 244866108 (100.00%) were paired; of these: 162645745 (66.42%) aligned concordantly 0 times 26306988 (10.74%) aligned concordantly exactly 1 time 55913375 (22.83%) aligned concordantly >1 times 33.58% overall alignment rate Processed 228000000 sequence pairs so far Processed 229000000 sequence pairs so far Processed 230000000 sequence pairs so far Processed 231000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2459:10023:27629_1:N:0:TTACAGGA+GCTTGTCA ptg000004l 1 Processed 232000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2461:29914:16703_1:N:0:TTACAGGA+ACTTGTCA ptg000082l 1 Processed 233000000 sequence pairs so far Processed 234000000 sequence pairs so far Processed 235000000 sequence pairs so far Processed 236000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2473:49740:27909_1:N:0:TTACAGGA+GCTTGTCA ptg000033l 2625591 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2475:29444:5440_1:N:0:TTACAGGA+GCTTGTCA ptg000077l 42446 Processed 237000000 sequence pairs so far Processed 238000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2478:12005:16296_1:N:0:TTACAGGA+GCTTGTCA ptg000033l 2625624 Processed 239000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2483:35546:11156_1:N:0:TTACAGGA+GCTTGTCA ptg000109l 39608 Processed 240000000 sequence pairs so far Processed 241000000 sequence pairs so far 244866108 reads; of these: 244866108 (100.00%) were paired; of these: 187127419 (76.42%) aligned concordantly 0 times 18975960 (7.75%) aligned concordantly exactly 1 time 38762729 (15.83%) aligned concordantly >1 times 23.58% overall alignment rate 244866108 reads; of these: 244866108 (100.00%) were paired; of these: 187014268 (76.37%) aligned concordantly 0 times 19062074 (7.78%) aligned concordantly exactly 1 time 38789766 (15.84%) aligned concordantly >1 times 23.63% overall alignment rate Processed 242000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2491:41850:6603_1:N:0:TTACAGGA+GCTTGTCA ptg000092l 1 Processed 243000000 sequence pairs so far Processed 244000000 sequence pairs so far 244866108 reads; of these: 244866108 (100.00%) were paired; of these: 162664302 (66.43%) aligned concordantly 0 times 26392181 (10.78%) aligned concordantly exactly 1 time 55809625 (22.79%) aligned concordantly >1 times 33.57% overall alignment rate Processed 244866108 sequences in total Successfully deleted the temporary files trimmed_ACR-145-TP2_S3_R1_001.fastq.gz_C_to_T.fastq, trimmed_ACR-145-TP2_S3_R1_001.fastq.gz_G_to_A.fastq, trimmed_ACR-145-TP2_S3_R2_001.fastq.gz_C_to_T.fastq and trimmed_ACR-145-TP2_S3_R2_001.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 244866108 Final Cytosine Methylation Report ================================= Total number of C's analysed: 5649675342 Total methylated C's in CpG context: 85511979 Total methylated C's in CHG context: 18977692 Total methylated C's in CHH context: 88350399 Total methylated C's in Unknown context: 16139487 Total unmethylated C's in CpG context: 878134725 Total unmethylated C's in CHG context: 1019570879 Total unmethylated C's in CHH context: 3559129668 Total unmethylated C's in Unknown context: 58014953 C methylated in CpG context: 8.9% C methylated in CHG context: 1.8% C methylated in CHH context: 2.4% C methylated in unknown context (CN or CHN): 21.8% Bismark completed in 1d 11h 50m 4s ==================== Bismark run complete ====================