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/F-Ptuh/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/F-Ptuh/code'): ../output/01.00-F-Ptuh-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POC-53-TP2_S15_R1_001.fastq.gz ../output/01.00-F-Ptuh-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POC-53-TP2_S15_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/F-Ptuh/output/12-Ptuh-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/F-Ptuh/code Now reading in and storing sequence information of the genome specified in: /scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/F-Ptuh/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-F-Ptuh-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POC-53-TP2_S15_R1_001.fastq.gz and ../output/01.00-F-Ptuh-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POC-53-TP2_S15_R2_001.fastq.gz Input files are in FastQ format Writing a C -> T converted version of the input file trimmed_POC-53-TP2_S15_R1_001.fastq.gz to trimmed_POC-53-TP2_S15_R1_001.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file trimmed_POC-53-TP2_S15_R1_001.fastq.gz to trimmed_POC-53-TP2_S15_R1_001.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file trimmed_POC-53-TP2_S15_R1_001.fastq.gz (141417553 sequences in total) Writing a C -> T converted version of the input file trimmed_POC-53-TP2_S15_R2_001.fastq.gz to trimmed_POC-53-TP2_S15_R2_001.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file trimmed_POC-53-TP2_S15_R2_001.fastq.gz to trimmed_POC-53-TP2_S15_R2_001.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file trimmed_POC-53-TP2_S15_R2_001.fastq.gz (141417553 sequences in total) Input files are trimmed_POC-53-TP2_S15_R1_001.fastq.gz_C_to_T.fastq and trimmed_POC-53-TP2_S15_R1_001.fastq.gz_G_to_A.fastq and trimmed_POC-53-TP2_S15_R2_001.fastq.gz_C_to_T.fastq and trimmed_POC-53-TP2_S15_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/F-Ptuh/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_POC-53-TP2_S15_R1_001.fastq.gz_C_to_T.fastq and trimmed_POC-53-TP2_S15_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: LH00260:131:22L7V3LT4:3:1101:3970:1014_1:N:0:ATGAGGCC+CNATTAAC/1 77 * 0 0 * * 0 0 TNTTTTAATTTTTTATATTAAATTTAAAAAATAAAAAATAAAAAATAAATAAAATTTTATAAAATTTTTATTAATAAAAATTAAAATTTTGTGGGA I#IIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII- YT:Z:UP LH00260:131:22L7V3LT4:3:1101:3970:1014_2:N:0:ATGAGGCC+CNATTAAC/2 141 * 0 0 * * 0 0 TNCCACAAAATTTTAATTTTTTTTAATAAAAATTTTATAAAATTTTATTTATTTTTTATTTTTTATTTTTTAAATTTAATATAAAAAATTAAAATA I#9IIII9IIIIII9III9IIIIIIIIIII99IIIIIIIII9IIIIIII9IIIIIIII99I9IIIII9IIIIIIIIIIIIII9III9II9II9III YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from trimmed_POC-53-TP2_S15_R1_001.fastq.gz_G_to_A.fastq and trimmed_POC-53-TP2_S15_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: LH00260:131:22L7V3LT4:3:1101:3970:1014_1:N:0:ATGAGGCC+CNATTAAC/1 77 * 0 0 * * 0 0 CNCCTTAATTCCTTACACTAAACTTAAAAAACAAAAAACAAAAAATAAATAAAATCCCACAAAATTTCCACCAACAAAAATTAAAATTTTATAAAA I#IIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII- YT:Z:UP LH00260:131:22L7V3LT4:3:1101:3970:1014_2:N:0:ATGAGGCC+CNATTAAC/2 141 * 0 0 * * 0 0 TNTTATAAAATTTTAATTTTTTTTGGTGGAAATTTTGTGGGATTTTATTTATTTTTTGTTTTTTGTTTTTTAAGTTTAGTGTAAGGAATTAAGGTG I#9IIII9IIIIII9III9IIIIIIIIIII99IIIIIIIII9IIIIIII9IIIIIIII99I9IIIII9IIIIIIIIIIIIII9III9II9II9III YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from trimmed_POC-53-TP2_S15_R1_001.fastq.gz_G_to_A.fastq and trimmed_POC-53-TP2_S15_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: LH00260:131:22L7V3LT4:3:1101:3970:1014_1:N:0:ATGAGGCC+CNATTAAC/1 83 Pocillopora_meandrina_HIv1___Sc0000033_CT_converted 3135942 40 6M1D90M = 3135942 -97 TTTTATAAAATTTTAATTTTTGTTGGTGGAAATTTTGTGGGATTTTATTTATTTTTTGTTTTTTGTTTTTTAAGTTTAGTGTAAGGAATTAAGGNG -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIII#I AS:i:-27 XN:i:0 XM:i:4 XO:i:1 XG:i:1 NM:i:5 MD:Z:0A5^G15T58A13T1 YS:i:-21 YT:Z:CP LH00260:131:22L7V3LT4:3:1101:3970:1014_2:N:0:ATGAGGCC+CNATTAAC/2 163 Pocillopora_meandrina_HIv1___Sc0000033_CT_converted 3135942 40 6M1D90M = 3135942 97 TNTTATAAAATTTTAATTTTTTTTGGTGGAAATTTTGTGGGATTTTATTTATTTTTTGTTTTTTGTTTTTTAAGTTTAGTGTAAGGAATTAAGGTG I#9IIII9IIIIII9III9IIIIIIIIIII99IIIIIIIII9IIIIIII9IIIIIIII99I9IIIII9IIIIIIIIIIIIII9III9II9II9III AS:i:-21 XN:i:0 XM:i:3 XO:i:1 XG:i:1 NM:i:4 MD:Z:0A0T4^G74A15 YS:i:-27 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from trimmed_POC-53-TP2_S15_R1_001.fastq.gz_C_to_T.fastq and trimmed_POC-53-TP2_S15_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: LH00260:131:22L7V3LT4:3:1101:3970:1014_1:N:0:ATGAGGCC+CNATTAAC/1 77 * 0 0 * * 0 0 TNTTTTAATTTTTTATATTAAATTTAAAAAATAAAAAATAAAAAATAAATAAAATTTTATAAAATTTTTATTAATAAAAATTAAAATTTTGTGGGA I#IIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII- YT:Z:UP LH00260:131:22L7V3LT4:3:1101:3970:1014_2:N:0:ATGAGGCC+CNATTAAC/2 141 * 0 0 * * 0 0 TNCCACAAAATTTTAATTTTTTTTAATAAAAATTTTATAAAATTTTATTTATTTTTTATTTTTTATTTTTTAAATTTAATATAAAAAATTAAAATA I#9IIII9IIIIII9III9IIIIIIIIIII99IIIIIIIII9IIIIIII9IIIIIIII99I9IIIII9IIIIIIIIIIIIII9III9II9II9III YT:Z:UP >>> Writing bisulfite mapping results to trimmed_POC-53-TP2_S15_pe.bam <<< Reading in the sequence files ../output/01.00-F-Ptuh-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POC-53-TP2_S15_R1_001.fastq.gz and ../output/01.00-F-Ptuh-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POC-53-TP2_S15_R2_001.fastq.gz Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1101:9699:15190_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000205 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1101:9707:15204_1:N:0:ATGAGGCA+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000205 1 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 LH00260:131:22L7V3LT4:3:1118:9966:25205_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___Sc0000037 2 Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1136:10622:14265_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___Sc0000057 1 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 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1162:10096:21872_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000974 1 Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1169:18706:18678_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000704 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1170:42651:24715_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___Sc0000023 5767015 Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1177:10290:26662_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000083 65166 Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1184:8493:10273_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000272 3 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1186:9667:12276_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000262 1 Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1194:48267:12332_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___Sc0000019 2 Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1209:10597:11562_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___Sc0000019 1 Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1213:43104:1602_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___Sc0000004 14584379 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1214:27785:15092_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000275 51869 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1215:36986:13565_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000527 44151 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1215:37002:13565_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000527 44151 Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1243:19402:4250_1:N:0:ATGAGGCC+CAATTGAC Pocillopora_meandrina_HIv1___xfSc0000621 1 Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1261:32875:28974_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000886 36217 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1266:31807:14461_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000817 37630 Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1285:9351:11310_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___Sc0000019 2 Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1293:5896:5160_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000205 1 Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1296:16173:28133_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___Sc0000068 3 Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1308:5604:3031_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000704 2 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 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1336:47716:5300_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000092 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1338:42351:4502_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000262 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1338:42902:10357_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000205 1 Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1352:46899:13551_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___Sc0000055 121478 Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1365:4674:3381_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000527 44103 Processed 48000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1369:13373:7009_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___Sc0000019 2 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1369:48380:12416_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000482 45434 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1370:6729:22432_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xpSc0001281 2 Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1381:38232:7458_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000272 3 Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1389:5022:13313_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___Sc0000004 14584379 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1390:42432:22712_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000083 65180 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1390:42448:22712_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000083 65180 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1390:12685:27867_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___Sc0000004 14584379 Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1404:42724:17137_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___Sc0000037 3 Processed 55000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1409:3679:5468_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000083 65166 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1409:3695:5468_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000083 65166 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1410:33927:8354_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000205 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1412:16537:17361_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000272 3 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1413:45969:16787_1:N:0:GTGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000205 1 Processed 56000000 sequence pairs so far Processed 57000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1420:3314:18370_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000704 2 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1423:10031:12991_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___Sc0000010 2 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 LH00260:131:22L7V3LT4:3:1441:15922:4362_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___Sc0000019 1 Processed 62000000 sequence pairs so far 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 Processed 70000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1489:22072:18061_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000262 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1489:22080:18075_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000262 1 Processed 71000000 sequence pairs so far Processed 72000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2105:3792:4404_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000343 3 Processed 73000000 sequence pairs so far Processed 74000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2116:29930:22250_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000565 3 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2118:35133:12374_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000704 2 Processed 75000000 sequence pairs so far Processed 76000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2130:42602:10847_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000704 2 Processed 77000000 sequence pairs so far Processed 78000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2144:29736:2807_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000621 1 Processed 79000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2146:49311:16913_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000343 3 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2146:49303:16927_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000343 3 Processed 80000000 sequence pairs so far Processed 81000000 sequence pairs so far Processed 82000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2163:16642:26200_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000272 1 Processed 83000000 sequence pairs so far 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 LH00260:131:22L7V3LT4:3:2181:46786:3914_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000083 65190 Processed 87000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2187:24678:9769_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___Sc0000082 32519 Processed 88000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2195:50411:24701_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000621 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2195:50427:24701_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000621 1 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 LH00260:131:22L7V3LT4:3:2222:32018:17291_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000205 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2223:10986:8480_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000566 1 Processed 94000000 sequence pairs so far Processed 95000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2233:5176:19770_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000262 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2234:29404:24085_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___Sc0000057 2 Processed 96000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2242:34356:22908_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___Sc0000019 2 Processed 97000000 sequence pairs so far Processed 98000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2252:14109:7752_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___Sc0000037 3 Processed 99000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2255:29784:16591_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000566 1 Processed 100000000 sequence pairs so far Processed 101000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2268:46834:27699_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000621 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2271:47555:7822_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___Sc0000004 14584379 Processed 102000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2273:19094:19210_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000621 1 Processed 103000000 sequence pairs so far Processed 104000000 sequence pairs so far Processed 105000000 sequence pairs so far Processed 106000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2301:50743:19532_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000262 1 Processed 107000000 sequence pairs so far Processed 108000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2314:22202:27026_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___Sc0000057 3 Processed 109000000 sequence pairs so far Processed 110000000 sequence pairs so far Processed 111000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2327:50322:9587_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___Sc0000037 3 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2329:50541:19518_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000621 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2331:45863:10245_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000817 37630 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2331:32276:21465_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xpSc0001355 2 Processed 112000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2336:21214:7696_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000272 2 Processed 113000000 sequence pairs so far Processed 114000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2349:17994:1224_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___Sc0000005 14098816 Processed 115000000 sequence pairs so far Processed 116000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2357:21935:8494_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000205 2 Processed 117000000 sequence pairs so far Processed 118000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2370:35360:26662_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000272 3 Processed 119000000 sequence pairs so far Processed 120000000 sequence pairs so far 141417553 reads; of these: 141417553 (100.00%) were paired; of these: 103811970 (73.41%) aligned concordantly 0 times 19163392 (13.55%) aligned concordantly exactly 1 time 18442191 (13.04%) aligned concordantly >1 times 26.59% overall alignment rate Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2380:50541:20415_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000083 65174 Processed 121000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2383:47085:11520_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000885 36284 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2386:42157:21956_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000817 37711 Processed 122000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2392:38532:11198_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___Sc0000037 1 Processed 123000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2396:17282:29212_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000083 65178 Processed 124000000 sequence pairs so far Processed 125000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2412:27025:20359_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___Sc0000004 14584379 Processed 126000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2419:47401:3101_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___Sc0000019 1 Processed 127000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2422:33871:13943_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___Sc0000037 3 Processed 128000000 sequence pairs so far Processed 129000000 sequence pairs so far Processed 130000000 sequence pairs so far 141417553 reads; of these: 141417553 (100.00%) were paired; of these: 106255259 (75.14%) aligned concordantly 0 times 17563849 (12.42%) aligned concordantly exactly 1 time 17598445 (12.44%) aligned concordantly >1 times 24.86% overall alignment rate Processed 131000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2445:3808:17627_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___Sc0000055 121536 141417553 reads; of these: 141417553 (100.00%) were paired; of these: 108919062 (77.02%) aligned concordantly 0 times 16601855 (11.74%) aligned concordantly exactly 1 time 15896636 (11.24%) aligned concordantly >1 times 22.98% overall alignment rate Processed 132000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2453:49375:7724_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000021 3 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 141417553 reads; of these: 141417553 (100.00%) were paired; of these: 109808910 (77.65%) aligned concordantly 0 times 16064364 (11.36%) aligned concordantly exactly 1 time 15544279 (10.99%) aligned concordantly >1 times 22.35% overall alignment rate Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2477:34348:23931_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000704 2 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2479:49796:18846_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___Sc0000019 1 Processed 138000000 sequence pairs so far Processed 139000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2487:3080:15330_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000704 3 Processed 140000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2495:9683:2555_1:N:0:ATGAGGCC+CAATTAAC Pocillopora_meandrina_HIv1___xfSc0000083 65168 Processed 141000000 sequence pairs so far Processed 141417553 sequences in total Successfully deleted the temporary files trimmed_POC-53-TP2_S15_R1_001.fastq.gz_C_to_T.fastq, trimmed_POC-53-TP2_S15_R1_001.fastq.gz_G_to_A.fastq, trimmed_POC-53-TP2_S15_R2_001.fastq.gz_C_to_T.fastq and trimmed_POC-53-TP2_S15_R2_001.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 141417553 Final Cytosine Methylation Report ================================= Total number of C's analysed: 3026230854 Total methylated C's in CpG context: 22895388 Total methylated C's in CHG context: 16320787 Total methylated C's in CHH context: 58134446 Total methylated C's in Unknown context: 7696769 Total unmethylated C's in CpG context: 533555765 Total unmethylated C's in CHG context: 606361912 Total unmethylated C's in CHH context: 1788962556 Total unmethylated C's in Unknown context: 36081212 C methylated in CpG context: 4.1% C methylated in CHG context: 2.6% C methylated in CHH context: 3.1% C methylated in unknown context (CN or CHN): 17.6% Bismark completed in 0d 10h 14m 21s ==================== Bismark run complete ====================