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-150-TP2_S2_R1_001.fastq.gz ../output/01.00-D-Apul-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_ACR-150-TP2_S2_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-150-TP2_S2_R1_001.fastq.gz and ../output/01.00-D-Apul-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_ACR-150-TP2_S2_R2_001.fastq.gz Input files are in FastQ format Writing a C -> T converted version of the input file trimmed_ACR-150-TP2_S2_R1_001.fastq.gz to trimmed_ACR-150-TP2_S2_R1_001.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file trimmed_ACR-150-TP2_S2_R1_001.fastq.gz to trimmed_ACR-150-TP2_S2_R1_001.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file trimmed_ACR-150-TP2_S2_R1_001.fastq.gz (234083660 sequences in total) Writing a C -> T converted version of the input file trimmed_ACR-150-TP2_S2_R2_001.fastq.gz to trimmed_ACR-150-TP2_S2_R2_001.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file trimmed_ACR-150-TP2_S2_R2_001.fastq.gz to trimmed_ACR-150-TP2_S2_R2_001.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file trimmed_ACR-150-TP2_S2_R2_001.fastq.gz (234083660 sequences in total) Input files are trimmed_ACR-150-TP2_S2_R1_001.fastq.gz_C_to_T.fastq and trimmed_ACR-150-TP2_S2_R1_001.fastq.gz_G_to_A.fastq and trimmed_ACR-150-TP2_S2_R2_001.fastq.gz_C_to_T.fastq and trimmed_ACR-150-TP2_S2_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-150-TP2_S2_R1_001.fastq.gz_C_to_T.fastq and trimmed_ACR-150-TP2_S2_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: LH00260:131:22L7V3LT4:3:1101:1979:1014_1:N:0:CCGTGAAG+ANCCACTG/1 99 ntLink_8_CT_converted 18032370 1 73M = 18032370 73 ANTATAATTTAGTGAAATGTTGGATTGATGAATGTTGAGGATGTTTGAATTGTTTTGTGTGTTTGTTTGTTAA I#IIIIIIIIIIIIIIIIIIIIIIIIIIII99I9III9IIIIIIIII-II99IIII99III9I-II9IIIIII AS:i:-25 XS:i:-25 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:1T40T1A9A8A9 YS:i:-6 YT:Z:CP LH00260:131:22L7V3LT4:3:1101:1979:1014_2:N:0:CCGTGAAG+ANCCACTG/2 147 ntLink_8_CT_converted 18032370 1 73M = 18032370 -73 ATTATAATTTAGTGAAATGTTGGATTGATGAATGTTGAGGATGTATGAATTGTTATGTGTGTTAGTTTGTTAA I9IIIIIIIII9-9II-99IIII9IIIIIIII9I-99I-9999I9IIIIIII9-I9I9-I99IIIIIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:42T30 YS:i:-25 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from trimmed_ACR-150-TP2_S2_R1_001.fastq.gz_G_to_A.fastq and trimmed_ACR-150-TP2_S2_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: LH00260:131:22L7V3LT4:3:1101:1979:1014_1:N:0:CCGTGAAG+ANCCACTG/1 77 * 0 0 * * 0 0 ANCATAATTTAATAAAATATTAAATTAATAAATACTAAAAATATCTAAATTATTCTATATATTCATTTATTAA I#IIIIIIIIIIIIIIIIIIIIIIIIIIII99I9III9IIIIIIIII-II99IIII99III9I-II9IIIIII YT:Z:UP LH00260:131:22L7V3LT4:3:1101:1979:1014_2:N:0:CCGTGAAG+ANCCACTG/2 141 * 0 0 * * 0 0 TTAATAAATTAATATATATAATAATTTATATATTTTTAGTATTTATTAATTTAATATTTTATTAAATTATGAT IIIIIIIIIII99I-9I9I-9IIIIIII9I9999-I99-I9IIIIIIII9IIII99-II9-9IIIIIIIII9I YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from trimmed_ACR-150-TP2_S2_R1_001.fastq.gz_G_to_A.fastq and trimmed_ACR-150-TP2_S2_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: LH00260:131:22L7V3LT4:3:1101:1979:1014_1:N:0:CCGTGAAG+ANCCACTG/1 77 * 0 0 * * 0 0 ANCATAATTTAATAAAATATTAAATTAATAAATACTAAAAATATCTAAATTATTCTATATATTCATTTATTAA I#IIIIIIIIIIIIIIIIIIIIIIIIIIII99I9III9IIIIIIIII-II99IIII99III9I-II9IIIIII YT:Z:UP LH00260:131:22L7V3LT4:3:1101:1979:1014_2:N:0:CCGTGAAG+ANCCACTG/2 141 * 0 0 * * 0 0 TTAATAAATTAATATATATAATAATTTATATATTTTTAGTATTTATTAATTTAATATTTTATTAAATTATGAT IIIIIIIIIII99I-9I9I-9IIIIIII9I9999-I99-I9IIIIIIII9IIII99-II9-9IIIIIIIII9I YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from trimmed_ACR-150-TP2_S2_R1_001.fastq.gz_C_to_T.fastq and trimmed_ACR-150-TP2_S2_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: LH00260:131:22L7V3LT4:3:1101:1979:1014_1:N:0:CCGTGAAG+ANCCACTG/1 83 ptg000035l_GA_converted 1522201 1 73M = 1522201 -73 TTAACAAACAAACACACAAAACAATTCAAACATCCTCAACATTCATCAATCCAACATTTCACTAAATTATANT IIIIII9II-I9III99IIII99II-IIIIIIIII9III9I99IIIIIIIIIIIIIIIIIIIIIIIIIIII#I AS:i:-19 XS:i:-19 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:9T8T9T42A1 YS:i:0 YT:Z:CP LH00260:131:22L7V3LT4:3:1101:1979:1014_2:N:0:CCGTGAAG+ANCCACTG/2 163 ptg000035l_GA_converted 1522201 1 73M = 1522201 73 TTAACAAACTAACACACATAACAATTCATACATCCTCAACATTCATCAATCCAACATTTCACTAAATTATAAT IIIIIIIIIII99I-9I9I-9IIIIIII9I9999-I99-I9IIIIIIII9IIII99-II9-9IIIIIIIII9I AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:73 YS:i:-19 YT:Z:CP >>> Writing bisulfite mapping results to trimmed_ACR-150-TP2_S2_pe.bam <<< Reading in the sequence files ../output/01.00-D-Apul-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_ACR-150-TP2_S2_R1_001.fastq.gz and ../output/01.00-D-Apul-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_ACR-150-TP2_S2_R2_001.fastq.gz Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1101:8437:15162_1:N:0:CCGTGAAG+ATCCACTG ptg000109l 39662 Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1104:25884:23118_1:N:0:CCGTGAAG+ATCCACTG ptg000093l 1 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1107:47579:28679_1:N:0:CCGTGAAG+ATCCACTG ptg000028l 618554 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1109:13875:24631_1:N:0:CCGTGAAG+ATCCACTG ptg000109l 39649 Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1114:3735:24169_1:N:0:CCGTGAAG+ATCCACTG ptg000093l 1 Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1118:27680:20737_1:N:0:CCGTGAAG+ATCCACTG ptg000069l 259876 Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1125:4682:27937_1:N:0:CCGTGAAG+ATCCACTG ptg000016l 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1126:29420:1196_1:N:0:CCGTGAAG+ATCCACTG ptg000090l 1 Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1128:31823:25051_1:N:0:CCGTGAAG+ATCCACTG ptg000108l 75314 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 LH00260:131:22L7V3LT4:3:1142:48971:3718_1:N:0:CCGTGAAG+ATCCACTG ptg000127l 27777 Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1156:27534:24715_1:N:0:CCGTGAAG+ATCCACTG ptg000113l 2 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1156:27543:24729_1:N:0:CCGTGAAG+ATCCACTG ptg000113l 2 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1158:20980:7318_1:N:0:CCGTGAAG+ATCCACTG ptg000033l 2625578 Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1159:45499:5805_1:N:0:CCGTGAAG+ATCCACTG ptg000033l 2625572 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1159:50460:25289_1:N:0:CCGTGAAG+ATCCACTG ptg000033l 2625658 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 LH00260:131:22L7V3LT4:3:1169:48501:5931_1:N:0:CCGTGAAG+ATCCACTG ptg000093l 1 Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1180:25269:8998_1:N:0:CCGTGAAG+ATCCACTG ptg000033l 2625658 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 Processed 29000000 sequence pairs so far 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 LH00260:131:22L7V3LT4:3:1209:44666:11982_1:N:0:CCGTGAAG+ATCCACTG ptg000112l 35516 Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1223:45944:18958_1:N:0:CCGTGAAG+ATCCACTG ptg000009l 19095960 Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1257:12499:13761_1:N:0:CCGTGAAG+ATCCACTG ptg000126l 1 Processed 47000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1261:23116:26452_1:N:0:CCGTGAAG+ATCCACTG ptg000109l 39639 Processed 48000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1265:26159:20149_1:N:0:CCGTGAAG+ATCCACTG ptg000069l 259787 Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1284:44698:6127_1:N:0:CCGTGAAG+ATCCACTG ptg000069l 259876 Processed 55000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1287:17184:12122_1:N:0:CCGTGAAG+ATCCACTG ptg000025l 21443060 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 Processed 62000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1311:28659:15876_1:N:0:CCGTGAAG+ATCCACTG ptg000095l 40204 Processed 63000000 sequence pairs so far 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 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1334:12022:3493_1:N:0:CCGTGAAG+ATCCACTG ptg000033l 2625657 Processed 70000000 sequence pairs so far Processed 71000000 sequence pairs so far 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 LH00260:131:22L7V3LT4:3:1353:38888:2457_1:N:0:CCGTGAAG+ATCCACTG ptg000033l 2625572 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1353:22412:9881_1:N:0:CCGTGAAG+ATCCACTG ptg000109l 39596 Processed 75000000 sequence pairs so far Processed 76000000 sequence pairs so far Processed 77000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1361:49181:29716_1:N:0:CNGTGAAG+NTCCACTG ptg000126l 1 Processed 78000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1364:30173:29282_1:N:0:CCGTGAAG+ATCCACTG ptg000109l 39590 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1365:45572:23468_1:N:0:CCGTGAAG+ATCCACTG ptg000093l 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1366:1647:14840_1:N:0:CCGTGAAG+ATCCACTG ptg000093l 1 Processed 79000000 sequence pairs so far Processed 80000000 sequence pairs so far Processed 81000000 sequence pairs so far Processed 82000000 sequence pairs so far Processed 83000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1382:8299:3185_1:N:0:CCGTGAAG+ATCCACTG ptg000105l 1 Processed 84000000 sequence pairs so far Processed 85000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1387:4836:13523_1:N:0:CCGTGAAG+ATCCACTG ptg000007l 12295845 Processed 86000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1391:20599:27559_1:N:0:CCGTGAAG+ATCCACTG ptg000033l 2625576 Processed 87000000 sequence pairs so far Processed 88000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1396:2691:27489_1:N:0:CCGTGAAG+ATCCACTG ptg000095l 40205 Processed 89000000 sequence pairs so far Processed 90000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1406:32811:3255_1:N:0:TCGTGAAG+ATCCACTG ptg000082l 1 Processed 91000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1408:40611:19420_1:N:0:CCGTGAAG+ATCCACTG ptg000109l 39589 Processed 92000000 sequence pairs so far Processed 93000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1414:34534:25682_1:N:0:CCGTGAAG+ATCCACTG ptg000095l 40204 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1416:24532:23468_1:N:0:CCGTGAAG+ATCCACTG ptg000027l 1 Processed 94000000 sequence pairs so far Processed 95000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1422:20154:22726_1:N:0:CCGTGAAG+ATCCACTG ptg000033l 2625657 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1422:4350:28875_1:N:0:CCGTGAAG+ATCCACTG ptg000093l 1 Processed 96000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1426:18139:23244_1:N:0:CCGTGAAG+ATCCACTG ptg000109l 39590 Processed 97000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1427:9489:16339_1:N:0:CCGTGAAG+ATCCACTG ptg000069l 259768 Processed 98000000 sequence pairs so far Processed 99000000 sequence pairs so far Processed 100000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1439:49011:11744_1:N:0:CCGTGAAG+ATCCACTG ptg000117l 29998 Processed 101000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1440:46041:4054_1:N:0:CCGTGAAG+ATCCACTG ntLink_1 163066 Processed 102000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1446:11301:8074_1:N:0:CCGTGAAG+ATCCACTG ptg000109l 39662 Processed 103000000 sequence pairs so far Processed 104000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1451:39616:21816_1:N:0:CCGTGAAG+ATCCACTG ptg000109l 39590 Processed 105000000 sequence pairs so far Processed 106000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1457:45532:17515_1:N:0:CCGTGAAG+ATCCACTG ptg000009l 19095978 Processed 107000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1461:10031:20863_1:N:0:CCGTGAAG+ATCCACTG ptg000135l 2 Processed 108000000 sequence pairs so far Processed 109000000 sequence pairs so far Processed 110000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1470:36347:22712_1:N:0:CCGTGAAG+ATCCACTG ptg000023l 2 Processed 111000000 sequence pairs so far Processed 112000000 sequence pairs so far Processed 113000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1480:21036:23553_1:N:0:CCGTGAAG+ATCCACTG ptg000109l 39569 Processed 114000000 sequence pairs so far Processed 115000000 sequence pairs so far Processed 116000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1489:24476:11016_1:N:0:CCGTGAAG+ATCCACTG ptg000146l 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1489:40539:27167_1:N:0:CCGTGAAG+ATCCACTG ptg000053l 71533 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1489:40531:27181_1:N:0:CCGTGAAG+ATCCACTG ptg000053l 71533 Processed 117000000 sequence pairs so far Processed 118000000 sequence pairs so far Processed 119000000 sequence pairs so far Processed 120000000 sequence pairs so far Processed 121000000 sequence pairs so far Processed 122000000 sequence pairs so far Processed 123000000 sequence pairs so far Processed 124000000 sequence pairs so far Processed 125000000 sequence pairs so far Processed 126000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2129:13931:3213_1:N:0:CCGTGAAG+ATCCACTG ptg000007l 12295850 Processed 127000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2130:24346:2751_1:N:0:CCGTGAAG+ATCCACTG ptg000105l 1 Processed 128000000 sequence pairs so far Processed 129000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2137:17597:3199_1:N:0:CCGTGAAG+ATCCACTG ptg000007l 12295845 Processed 130000000 sequence pairs so far Processed 131000000 sequence pairs so far Processed 132000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2147:9788:20583_1:N:0:CCGTGAAG+ATCCACTG ptg000122l 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2148:17516:14321_1:N:0:CCGTGAAG+ATCCACTG ptg000109l 39608 Processed 133000000 sequence pairs so far Processed 134000000 sequence pairs so far Processed 135000000 sequence pairs so far Processed 136000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2162:38103:26088_1:N:0:CCGTGAAG+ATCCACTG ptg000033l 2625657 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2162:38119:26088_1:N:0:CCGTGAAG+ATCCACTG ptg000033l 2625657 Processed 137000000 sequence pairs so far Processed 138000000 sequence pairs so far Processed 139000000 sequence pairs so far Processed 140000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2172:41332:29604_1:N:0:CCGTGAAG+ATCCACTG ptg000033l 2625657 Processed 141000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2177:50355:4432_1:N:0:CCGTGAAG+ATCCACTG ptg000109l 39662 Processed 142000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2180:29800:21942_1:N:0:CCGTGAAG+ATCCACTG ptg000122l 1 Processed 143000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2182:40806:29590_1:N:0:CCGTGAAG+ATCCACTG ptg000109l 39608 Processed 144000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2185:36315:29380_1:N:0:CCGTGAAG+ATCCACTG ptg000036l 6407170 Processed 145000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2187:22291:29702_1:N:0:NCGTGAAG+NTCCACTG ptg000069l 259767 Processed 146000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2190:12159:29338_1:N:0:CCGTGAAG+ATCCACTG ptg000004l 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2190:12151:29352_1:N:0:CCGTGAAG+ATCCACTG ptg000004l 1 Processed 147000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2194:48566:22068_1:N:0:CCGTGAAG+ATCCACTG ptg000033l 2625580 Processed 148000000 sequence pairs so far Processed 149000000 sequence pairs so far Processed 150000000 sequence pairs so far Processed 151000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2212:47466:13831_1:N:0:CCGTGAAG+ATCCACTG ptg000109l 39608 Processed 152000000 sequence pairs so far Processed 153000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2217:50767:9040_1:N:0:CCGTGAAG+ATCCACTG ptg000033l 2625572 Processed 154000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2221:13535:17907_1:N:0:CCGTGGAG+ATCCACTG ptg000117l 30028 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2222:24217:17095_1:N:0:CCGTGAAG+ATCCACTG ptg000109l 39636 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2223:27551:6757_1:N:0:CCGTGAAG+ATCCACTG ptg000033l 2625573 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2223:27543:6771_1:N:0:CCGTGAAG+ATCCACTG ptg000033l 2625573 Processed 155000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2227:12653:4726_1:N:0:CCGTGAAG+ATCCACTG ptg000069l 259768 Processed 156000000 sequence pairs so far Processed 157000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2233:29323:20163_1:N:0:CCGTGAAG+ATCCACTG ptg000109l 39649 Processed 158000000 sequence pairs so far Processed 159000000 sequence pairs so far Processed 160000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2242:41348:10805_1:N:0:CCGTGAAG+ATCCACTG ptg000033l 2625620 Processed 161000000 sequence pairs so far Processed 162000000 sequence pairs so far Processed 163000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2254:26248:14644_1:N:0:CCGTGAAG+ATCCACTG ptg000002l 1 Processed 164000000 sequence pairs so far Processed 165000000 sequence pairs so far Processed 166000000 sequence pairs so far Processed 167000000 sequence pairs so far Processed 168000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2271:16173:19588_1:N:0:CCGTGAAG+ATCCACTG ptg000117l 30028 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2271:16189:19588_1:N:0:CCGTGAAG+ATCCACTG ptg000117l 30028 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2271:4779:22334_1:N:0:CCGTGAAG+ATCCACTG ptg000008l 38432900 Processed 169000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2272:11471:24001_1:N:0:CCGTGAAG+ATCCACTG ptg000027l 16268220 Processed 170000000 sequence pairs so far Processed 171000000 sequence pairs so far Processed 172000000 sequence pairs so far Processed 173000000 sequence pairs so far Processed 174000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2291:49561:15162_1:N:0:CCGTGAAG+ATCCACTG ptg000113l 1 Processed 175000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2293:17994:23693_1:N:0:CCGTGAAG+ATCCACTG ptg000033l 2625659 Processed 176000000 sequence pairs so far Processed 177000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2304:13826:16927_1:N:0:CCGTGAAG+ATCCACTG ptg000093l 1 Processed 178000000 sequence pairs so far Processed 179000000 sequence pairs so far Processed 180000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2314:44828:12430_1:N:0:CCGTGAAG+ATCCACTG ptg000009l 19095978 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2314:43152:12696_1:N:0:CCGTGAAG+ATCCACTG ptg000009l 19095978 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2314:43169:12696_1:N:0:CCGTGAAG+ATCCACTG ptg000009l 19095979 Processed 181000000 sequence pairs so far Processed 182000000 sequence pairs so far Processed 183000000 sequence pairs so far Processed 184000000 sequence pairs so far Processed 185000000 sequence pairs so far Processed 186000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2335:14012:11002_1:N:0:CCGTGAAG+ATCCACTG ptg000036l 6407154 Processed 187000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2338:13689:11226_1:N:0:CCGTGAAG+ATCCACTG ptg000126l 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2338:17727:23118_1:N:0:CCGTGAAG+ATCCACTG ptg000135l 3 Processed 188000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2343:19928:12080_1:N:0:CCGTGAAG+ATCCACTG ptg000090l 1 Processed 189000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2344:35360:24365_1:N:0:CCGTGAAG+ATCCACTG ptg000061l 1 Processed 190000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2349:40199:27671_1:N:0:CCGTGAAG+ATCCACTG ptg000033l 2625657 Processed 191000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2353:11463:13089_1:N:0:CCGTGAAG+ATCCACTG ptg000069l 259768 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2353:11471:13103_1:N:0:CCGTGAAG+ATCCACTG ptg000069l 259768 Processed 192000000 sequence pairs so far Processed 193000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2359:28069:22138_1:N:0:CCGTGAAG+ATCCACTG ptg000093l 1 Processed 194000000 sequence pairs so far Processed 195000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2365:50767:23076_1:N:0:CCGTGAAG+ATCCACTG ptg000109l 39608 Processed 196000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2368:36541:3858_1:N:0:CCGTGAAG+ATCCACTG ptg000033l 2625572 Processed 197000000 sequence pairs so far Processed 198000000 sequence pairs so far Processed 199000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2379:33790:28175_1:N:0:CCGTGAAG+ATCCACTG ptg000029c 2 Processed 200000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2382:10541:20989_1:N:0:CCGTGAAG+ATCCACTG ptg000009l 19095953 Processed 201000000 sequence pairs so far Processed 202000000 sequence pairs so far Processed 203000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2394:32697:13537_1:N:0:ACGTGAAG+ATCCACTG ptg000006l 1 Processed 204000000 sequence pairs so far Processed 205000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2403:17338:13845_1:N:0:CCGTGAAG+ATCCACTG ptg000006l 3 Processed 206000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2407:45135:3325_1:N:0:CCGTGAAG+ATCCACTG ptg000015l 14997082 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 LH00260:131:22L7V3LT4:3:2417:45499:28665_1:N:0:CCGTGAAG+ATCCACTG ptg000090l 1 Processed 210000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2419:39398:19644_1:N:0:CCGTGAAG+ATCCACTG ptg000092l 1 Processed 211000000 sequence pairs so far Processed 212000000 sequence pairs so far Processed 213000000 sequence pairs so far Processed 214000000 sequence pairs so far 234083660 reads; of these: 234083660 (100.00%) were paired; of these: 184440524 (78.79%) aligned concordantly 0 times 16124298 (6.89%) aligned concordantly exactly 1 time 33518838 (14.32%) aligned concordantly >1 times 21.21% overall alignment rate Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2437:38046:14251_1:N:0:CCGTGAAG+ATCCACTG ptg000109l 39608 Processed 215000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2437:21894:27307_1:N:0:CCGTGAAG+ATCCACTG ptg000036l 1 234083660 reads; of these: 234083660 (100.00%) were paired; of these: 157752849 (67.39%) aligned concordantly 0 times 24328371 (10.39%) aligned concordantly exactly 1 time 52002440 (22.22%) aligned concordantly >1 times 32.61% overall alignment rate Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2440:25285:18272_1:N:0:CCGTGAAG+ATCCACTG ptg000024l 12381218 Processed 216000000 sequence pairs so far Processed 217000000 sequence pairs so far Processed 218000000 sequence pairs so far Processed 219000000 sequence pairs so far Processed 220000000 sequence pairs so far Processed 221000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2459:51172:23356_1:N:0:CCGTGAAG+ATCCACTG ptg000033l 2625666 Processed 222000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2461:28465:18566_1:N:0:CCGTGAAG+ATCCACTG ptg000090l 1 Processed 223000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2465:26499:12304_1:N:0:CCGTGAAG+ATCCACTG ptg000109l 39649 Processed 224000000 sequence pairs so far Processed 225000000 sequence pairs so far Processed 226000000 sequence pairs so far Processed 227000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2476:24120:9727_1:N:0:CCGTGAAG+ATCCACTG ptg000008l 38432912 Processed 228000000 sequence pairs so far Processed 229000000 sequence pairs so far 234083660 reads; of these: 234083660 (100.00%) were paired; of these: 184379674 (78.77%) aligned concordantly 0 times 16164490 (6.91%) aligned concordantly exactly 1 time 33539496 (14.33%) aligned concordantly >1 times 21.23% overall alignment rate 234083660 reads; of these: 234083660 (100.00%) were paired; of these: 157624239 (67.34%) aligned concordantly 0 times 24441848 (10.44%) aligned concordantly exactly 1 time 52017573 (22.22%) aligned concordantly >1 times 32.66% overall alignment rate Processed 230000000 sequence pairs so far Processed 231000000 sequence pairs so far Processed 232000000 sequence pairs so far Processed 233000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2497:37706:7556_1:N:0:CCGTGAAG+ATCCACTG ptg000027l 1 Processed 234000000 sequence pairs so far Processed 234083660 sequences in total Successfully deleted the temporary files trimmed_ACR-150-TP2_S2_R1_001.fastq.gz_C_to_T.fastq, trimmed_ACR-150-TP2_S2_R1_001.fastq.gz_G_to_A.fastq, trimmed_ACR-150-TP2_S2_R2_001.fastq.gz_C_to_T.fastq and trimmed_ACR-150-TP2_S2_R2_001.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 234083660 Final Cytosine Methylation Report ================================= Total number of C's analysed: 4826708375 Total methylated C's in CpG context: 89607039 Total methylated C's in CHG context: 18299207 Total methylated C's in CHH context: 86677563 Total methylated C's in Unknown context: 13932902 Total unmethylated C's in CpG context: 742472247 Total unmethylated C's in CHG context: 882032802 Total unmethylated C's in CHH context: 3007619517 Total unmethylated C's in Unknown context: 48070600 C methylated in CpG context: 10.8% C methylated in CHG context: 2.0% C methylated in CHH context: 2.8% C methylated in unknown context (CN or CHN): 22.5% Bismark completed in 1d 23h 45m 46s ==================== Bismark run complete ====================