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-48-TP2_S11_R1_001.fastq.gz ../output/01.00-F-Ptuh-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POC-48-TP2_S11_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-48-TP2_S11_R1_001.fastq.gz and ../output/01.00-F-Ptuh-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POC-48-TP2_S11_R2_001.fastq.gz Input files are in FastQ format Writing a C -> T converted version of the input file trimmed_POC-48-TP2_S11_R1_001.fastq.gz to trimmed_POC-48-TP2_S11_R1_001.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file trimmed_POC-48-TP2_S11_R1_001.fastq.gz to trimmed_POC-48-TP2_S11_R1_001.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file trimmed_POC-48-TP2_S11_R1_001.fastq.gz (177078360 sequences in total) Writing a C -> T converted version of the input file trimmed_POC-48-TP2_S11_R2_001.fastq.gz to trimmed_POC-48-TP2_S11_R2_001.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file trimmed_POC-48-TP2_S11_R2_001.fastq.gz to trimmed_POC-48-TP2_S11_R2_001.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file trimmed_POC-48-TP2_S11_R2_001.fastq.gz (177078360 sequences in total) Input files are trimmed_POC-48-TP2_S11_R1_001.fastq.gz_C_to_T.fastq and trimmed_POC-48-TP2_S11_R1_001.fastq.gz_G_to_A.fastq and trimmed_POC-48-TP2_S11_R2_001.fastq.gz_C_to_T.fastq and trimmed_POC-48-TP2_S11_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-48-TP2_S11_R1_001.fastq.gz_C_to_T.fastq and trimmed_POC-48-TP2_S11_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: LH00260:131:22L7V3LT4:3:1101:2125:1014_1:N:0:ACTAAGGT+CNGCGGTT/1 99 Pocillopora_meandrina_HIv1___Sc0000028_CT_converted 1569683 22 52M = 1569683 52 TNTTTGTTTATGGTGATGATGGTATTTTTTTAAAAATGATAAGTTATTTGTT I#IIIIIII9IIIIIIIIIII-IIIIIIIIIIIII9IIIIIIIII9IIIIII AS:i:-7 XS:i:-43 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:0G0T50 YS:i:-6 YT:Z:CP LH00260:131:22L7V3LT4:3:1101:2125:1014_2:N:0:ACTAAGGT+CNGCGGTT/2 147 Pocillopora_meandrina_HIv1___Sc0000028_CT_converted 1569683 22 52M = 1569683 -52 TTTTTGTTTATGGTGATGATGGTATTTTTTTAAAAATGATAAGTTATTTGTT I9IIIIII9IIIIIIIIII99IIIIII9IIIIIIIIIIIIII-IIIIIIIII AS:i:-6 XS:i:-42 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:0G51 YS:i:-7 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from trimmed_POC-48-TP2_S11_R1_001.fastq.gz_G_to_A.fastq and trimmed_POC-48-TP2_S11_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: LH00260:131:22L7V3LT4:3:1101:2125:1014_1:N:0:ACTAAGGT+CNGCGGTT/1 77 * 0 0 * * 0 0 CNTTTATTTATAATAATAATAATATTTTTTTAAAAATAATAAATTATTTATT I#IIIIIII9IIIIIIIIIII-IIIIIIIIIIIII9IIIIIIIII9IIIIII YT:Z:UP LH00260:131:22L7V3LT4:3:1101:2125:1014_2:N:0:ACTAAGGT+CNGCGGTT/2 141 * 0 0 * * 0 0 AATAAATAATTTATTATTTTTAAAAAAATATTATTATTATTATAAATAAAAG IIIIIIIII-IIIIIIIIIIIIII9IIIIII99IIIIIIIIII9IIIIII9I YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from trimmed_POC-48-TP2_S11_R1_001.fastq.gz_G_to_A.fastq and trimmed_POC-48-TP2_S11_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: LH00260:131:22L7V3LT4:3:1101:2125:1014_1:N:0:ACTAAGGT+CNGCGGTT/1 77 * 0 0 * * 0 0 CNTTTATTTATAATAATAATAATATTTTTTTAAAAATAATAAATTATTTATT I#IIIIIII9IIIIIIIIIII-IIIIIIIIIIIII9IIIIIIIII9IIIIII YT:Z:UP LH00260:131:22L7V3LT4:3:1101:2125:1014_2:N:0:ACTAAGGT+CNGCGGTT/2 141 * 0 0 * * 0 0 AATAAATAATTTATTATTTTTAAAAAAATATTATTATTATTATAAATAAAAG IIIIIIIII-IIIIIIIIIIIIII9IIIIII99IIIIIIIIII9IIIIII9I YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from trimmed_POC-48-TP2_S11_R1_001.fastq.gz_C_to_T.fastq and trimmed_POC-48-TP2_S11_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: LH00260:131:22L7V3LT4:3:1101:2125:1014_1:N:0:ACTAAGGT+CNGCGGTT/1 77 * 0 0 * * 0 0 TNTTTGTTTATGGTGATGATGGTATTTTTTTAAAAATGATAAGTTATTTGTT I#IIIIIII9IIIIIIIIIII-IIIIIIIIIIIII9IIIIIIIII9IIIIII YT:Z:UP LH00260:131:22L7V3LT4:3:1101:2125:1014_2:N:0:ACTAAGGT+CNGCGGTT/2 141 * 0 0 * * 0 0 AACAAATAACTTATCATTTTTAAAAAAATACCATCATCACCATAAACAAAAA IIIIIIIII-IIIIIIIIIIIIII9IIIIII99IIIIIIIIII9IIIIII9I YT:Z:UP >>> Writing bisulfite mapping results to trimmed_POC-48-TP2_S11_pe.bam <<< Reading in the sequence files ../output/01.00-F-Ptuh-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POC-48-TP2_S11_R1_001.fastq.gz and ../output/01.00-F-Ptuh-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POC-48-TP2_S11_R2_001.fastq.gz Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1101:46049:13313_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000527 44088 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1101:46041:13327_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000527 44088 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1104:22695:28161_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000019 1 Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1108:23108:10245_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xpSc0001355 1 Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1114:18601:22194_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000704 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1117:33806:1644_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000272 3 Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1123:46308:9587_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000428 1 Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1129:22533:14966_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xpSc0001355 2 Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1137:40741:4040_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000005 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1139:38168:17011_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000062 74043 Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1139:29468:25654_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000004 14584367 Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1145:31807:15134_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000704 2 Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1157:4164:21017_1:N:0:ACTAAGAT+GCGCGGTT Pocillopora_meandrina_HIv1___xpSc0001355 2 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1157:4156:21031_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xpSc0001355 2 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1158:43735:7570_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000704 2 Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1164:22776:11772_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000272 3 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1164:18916:17697_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000045 3 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1165:20696:2485_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000272 3 Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1170:12540:11226_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000068 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 LH00260:131:22L7V3LT4:3:1183:4714:23230_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000301 50660 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1183:4722:23244_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000301 50660 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1186:36549:25360_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000055 121477 Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1193:33984:6323_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000527 44088 Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1198:4706:26018_1:N:0:ACTAAGAT+CCGTGGTT Pocillopora_meandrina_HIv1___Sc0000019 2 Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1203:50330:25962_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xpSc0001355 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1204:4350:3970_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000092 1 Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1211:26863:4026_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000995 3 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 LH00260:131:22L7V3LT4:3:1224:33523:20513_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000301 50669 Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1231:21579:6729_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000272 3 Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1236:33474:6281_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xpSc0001355 1 Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1236:21117:20303_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000057 1 Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1253:36776:1210_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000272 3 Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1255:24791:14251_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000004 14584367 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 LH00260:131:22L7V3LT4:3:1267:3598:26480_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000004 14584367 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1267:3590:26494_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000004 14584367 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1268:5281:8298_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xpSc0001355 2 Processed 39000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1271:43371:26158_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000817 3 Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1278:48234:18468_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000343 3 Processed 41000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1283:13834:19042_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000010 1 Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1287:44010:7906_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000019 2 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1287:12167:22236_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000092 1 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 LH00260:131:22L7V3LT4:3:1303:44949:19392_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000479 45655 Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1315:3889:18075_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000005 1 Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1324:20090:22138_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xpSc0001355 1 Processed 51000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1327:39131:27054_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000788 2 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 LH00260:131:22L7V3LT4:3:1342:15339:23833_1:N:0:ACTAAGAT+TCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000704 1 Processed 55000000 sequence pairs so far 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 LH00260:131:22L7V3LT4:3:1375:31046:11380_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000301 50665 Processed 63000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1378:37140:10301_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xpSc0001355 2 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1378:18390:28273_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000704 2 Processed 64000000 sequence pairs so far Processed 65000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1387:17775:26900_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xpSc0001355 1 Processed 66000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1391:7247:23553_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000068 2 Processed 67000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1396:45046:26172_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000004 14584367 Processed 68000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1404:8226:13117_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000262 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1404:8243:13117_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000262 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1404:8234:13131_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000262 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1404:33272:19266_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xpSc0001355 2 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 LH00260:131:22L7V3LT4:3:1415:41048:24855_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xpSc0001355 2 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1417:44115:20247_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000004 14584367 Processed 72000000 sequence pairs so far Processed 73000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1423:39220:23651_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000596 1 Processed 74000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1428:42902:29604_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000019 1 Processed 75000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1433:23027:10273_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000704 1 Processed 76000000 sequence pairs so far Processed 77000000 sequence pairs so far Processed 78000000 sequence pairs so far Processed 79000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1449:6219:29338_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000301 50665 Processed 80000000 sequence pairs so far Processed 81000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1460:50937:13397_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000019 2 Processed 82000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1462:32705:4362_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000228 2 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1464:11957:15596_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000016 9288050 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1464:11965:15610_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000016 9288049 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1464:11981:15610_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000016 9288049 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1464:11973:15624_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000016 9288049 Processed 83000000 sequence pairs so far Processed 84000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1471:3379:28651_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000045 3 Processed 85000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1474:12985:6337_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xpSc0001344 5596 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1474:2400:21577_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000010 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1477:9699:2723_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000428 1 Processed 86000000 sequence pairs so far Processed 87000000 sequence pairs so far Processed 88000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1487:36258:26116_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000057 3 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1489:30237:15638_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000016 9288028 Processed 89000000 sequence pairs so far Processed 90000000 sequence pairs so far Processed 91000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2104:50597:4040_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xpSc0001355 1 Processed 92000000 sequence pairs so far Processed 93000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2114:32163:4208_1:N:0:ACTAAGAT+TCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000621 3 Processed 94000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2116:40053:22488_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000004 14584367 Processed 95000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2122:15509:21325_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000055 121456 Processed 96000000 sequence pairs so far Processed 97000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2130:15736:20513_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000262 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2134:4205:4502_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000621 3 Processed 98000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2136:23707:6071_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000527 44148 Processed 99000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2142:25803:13089_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000621 1 Processed 100000000 sequence pairs so far Processed 101000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2150:13098:2947_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000045 2 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2150:13106:2961_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000045 2 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2150:46705:28231_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xpSc0001337 6635 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2152:46632:16142_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000005 1 Processed 102000000 sequence pairs so far Processed 103000000 sequence pairs so far Processed 104000000 sequence pairs so far Processed 105000000 sequence pairs so far Processed 106000000 sequence pairs so far Processed 107000000 sequence pairs so far Processed 108000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2179:35174:1658_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000016 9288061 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2179:35182:1672_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000016 9288061 Processed 109000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2182:8922:1378_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000447 2 Processed 110000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2187:45167:18089_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xpSc0001355 1 Processed 111000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2191:45685:21395_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000527 44119 Processed 112000000 sequence pairs so far 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 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2223:26555:13187_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000016 9288052 Processed 118000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2224:11746:5875_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000948 2 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2226:8874:7009_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000019 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2226:25592:21914_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000527 44105 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2227:47101:7037_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xpSc0001355 2 Processed 119000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2233:29679:4278_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000272 3 Processed 120000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2234:28247:12276_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000045 3 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 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2256:24476:24911_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000527 44088 Processed 126000000 sequence pairs so far Processed 127000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2265:32446:1644_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000004 14584367 Processed 128000000 sequence pairs so far Processed 129000000 sequence pairs so far Processed 130000000 sequence pairs so far Processed 131000000 sequence pairs so far Processed 132000000 sequence pairs so far 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 LH00260:131:22L7V3LT4:3:2312:35473:13747_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000343 3 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2313:24824:12486_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000704 1 Processed 137000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2316:23925:3115_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000005 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 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2333:31046:9671_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000262 3 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2336:23496:11758_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000092 1 Processed 142000000 sequence pairs so far Processed 143000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2345:29177:18005_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000272 3 Processed 144000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2348:4002:23987_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000621 1 Processed 145000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2351:17144:6365_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000527 44143 Processed 146000000 sequence pairs so far Processed 147000000 sequence pairs so far Processed 148000000 sequence pairs so far Processed 149000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2372:23529:23917_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xpSc0001355 2 Processed 150000000 sequence pairs so far Processed 151000000 sequence pairs so far Processed 152000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2383:49141:22306_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000566 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2386:27890:10455_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000083 65168 Processed 153000000 sequence pairs so far Processed 154000000 sequence pairs so far Processed 155000000 sequence pairs so far 177078360 reads; of these: 177078360 (100.00%) were paired; of these: 128360031 (72.49%) aligned concordantly 0 times 25254698 (14.26%) aligned concordantly exactly 1 time 23463631 (13.25%) aligned concordantly >1 times 27.51% overall alignment rate Processed 156000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2403:25528:22950_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000527 44104 177078360 reads; of these: 177078360 (100.00%) were paired; of these: 128390687 (72.51%) aligned concordantly 0 times 25180734 (14.22%) aligned concordantly exactly 1 time 23506939 (13.27%) aligned concordantly >1 times 27.49% overall alignment rate Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2408:18560:8312_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000055 121470 Processed 157000000 sequence pairs so far Processed 158000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2417:51471:16254_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000621 3 Processed 159000000 sequence pairs so far Processed 160000000 sequence pairs so far 177078360 reads; of these: 177078360 (100.00%) were paired; of these: 141333729 (79.81%) aligned concordantly 0 times 18536022 (10.47%) aligned concordantly exactly 1 time 17208609 (9.72%) aligned concordantly >1 times 20.19% overall alignment rate Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2426:46478:29744_1:N:0:NCTAAGAT+NCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000343 3 Processed 161000000 sequence pairs so far Processed 162000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2432:44480:21129_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000045 3 Processed 163000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2440:11471:7640_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000527 44104 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2441:26992:2933_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000004 14584379 Processed 164000000 sequence pairs so far Processed 165000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2446:24629:23553_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000004 14584367 Processed 166000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2452:11479:8802_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000037 2 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2453:4593:4978_1:N:0:ACTAAGAT+CCGTGGTT Pocillopora_meandrina_HIv1___Sc0000057 1 Processed 167000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2458:40215:15876_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xpSc0001355 1 Processed 168000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2461:19628:6211_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000004 14584367 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2461:19620:6225_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000004 14584367 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2461:28805:15428_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000005 1 Processed 169000000 sequence pairs so far Processed 170000000 sequence pairs so far Processed 171000000 sequence pairs so far Processed 172000000 sequence pairs so far Processed 173000000 sequence pairs so far 177078360 reads; of these: 177078360 (100.00%) were paired; of these: 141306036 (79.80%) aligned concordantly 0 times 18593498 (10.50%) aligned concordantly exactly 1 time 17178826 (9.70%) aligned concordantly >1 times 20.20% overall alignment rate Processed 174000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2485:33482:6771_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000019 1 Processed 175000000 sequence pairs so far Processed 176000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2494:31896:4362_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___Sc0000068 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2495:34097:16829_1:N:0:ACTAAGAT+CCGCGGTT Pocillopora_meandrina_HIv1___xfSc0000704 1 Processed 177000000 sequence pairs so far Processed 177078360 sequences in total Successfully deleted the temporary files trimmed_POC-48-TP2_S11_R1_001.fastq.gz_C_to_T.fastq, trimmed_POC-48-TP2_S11_R1_001.fastq.gz_G_to_A.fastq, trimmed_POC-48-TP2_S11_R2_001.fastq.gz_C_to_T.fastq and trimmed_POC-48-TP2_S11_R2_001.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 177078360 Final Cytosine Methylation Report ================================= Total number of C's analysed: 4027104417 Total methylated C's in CpG context: 26211877 Total methylated C's in CHG context: 14132535 Total methylated C's in CHH context: 73475503 Total methylated C's in Unknown context: 12765557 Total unmethylated C's in CpG context: 639104269 Total unmethylated C's in CHG context: 772862587 Total unmethylated C's in CHH context: 2501317646 Total unmethylated C's in Unknown context: 47337161 C methylated in CpG context: 3.9% C methylated in CHG context: 1.8% C methylated in CHH context: 2.9% C methylated in unknown context (CN or CHN): 21.2% Bismark completed in 0d 14h 42m 1s ==================== Bismark run complete ====================