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-50-TP2_S14_R1_001.fastq.gz ../output/01.00-F-Ptuh-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POC-50-TP2_S14_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-50-TP2_S14_R1_001.fastq.gz and ../output/01.00-F-Ptuh-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POC-50-TP2_S14_R2_001.fastq.gz Input files are in FastQ format Writing a C -> T converted version of the input file trimmed_POC-50-TP2_S14_R1_001.fastq.gz to trimmed_POC-50-TP2_S14_R1_001.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file trimmed_POC-50-TP2_S14_R1_001.fastq.gz to trimmed_POC-50-TP2_S14_R1_001.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file trimmed_POC-50-TP2_S14_R1_001.fastq.gz (167114293 sequences in total) Writing a C -> T converted version of the input file trimmed_POC-50-TP2_S14_R2_001.fastq.gz to trimmed_POC-50-TP2_S14_R2_001.fastq.gz_C_to_T.fastq Writing a G -> A converted version of the input file trimmed_POC-50-TP2_S14_R2_001.fastq.gz to trimmed_POC-50-TP2_S14_R2_001.fastq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file trimmed_POC-50-TP2_S14_R2_001.fastq.gz (167114293 sequences in total) Input files are trimmed_POC-50-TP2_S14_R1_001.fastq.gz_C_to_T.fastq and trimmed_POC-50-TP2_S14_R1_001.fastq.gz_G_to_A.fastq and trimmed_POC-50-TP2_S14_R2_001.fastq.gz_C_to_T.fastq and trimmed_POC-50-TP2_S14_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-50-TP2_S14_R1_001.fastq.gz_C_to_T.fastq and trimmed_POC-50-TP2_S14_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: LH00260:131:22L7V3LT4:3:1101:1510:1014_1:N:0:ACAGAATT+TNGCCGGT/1 77 * 0 0 * * 0 0 TNATTTAAAATTTAAAATTATAAATAATAATTTTTATATTATTAATAAAAATATTATAAA 9#IIIIIIIIII-II9IIII9IIII-III9IIII9-I-I9IIIIII9I99III9II-II9 YT:Z:UP LH00260:131:22L7V3LT4:3:1101:1510:1014_2:N:0:ACAGAATT+TNGCCGGT/2 141 * 0 0 * * 0 0 TTTATAATATTTTTATTAATAATATAAAAATTATTATTTTTAATTTTTAATTTTAAATAA IIIIII-IIIIIII9IIII-IIIIIII9I-I9--II-9I9IIII9I99I-I-III-9999 YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from trimmed_POC-50-TP2_S14_R1_001.fastq.gz_G_to_A.fastq and trimmed_POC-50-TP2_S14_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: LH00260:131:22L7V3LT4:3:1101:1510:1014_1:N:0:ACAGAATT+TNGCCGGT/1 77 * 0 0 * * 0 0 CNATTCAAAATTCAAAATTACAAACAATAATTTCCATACCATTAACAAAAATATCACAAA 9#IIIIIIIIII-II9IIII9IIII-III9IIII9-I-I9IIIIII9I99III9II-II9 YT:Z:UP LH00260:131:22L7V3LT4:3:1101:1510:1014_2:N:0:ACAGAATT+TNGCCGGT/2 141 * 0 0 * * 0 0 TTTGTGGTATTTTTGTTAATGGTATGGAAATTATTGTTTTTAATTTTTAATTTTGAATGG IIIIII-IIIIIII9IIII-IIIIIII9I-I9--II-9I9IIII9I99I-I-III-9999 YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from trimmed_POC-50-TP2_S14_R1_001.fastq.gz_G_to_A.fastq and trimmed_POC-50-TP2_S14_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: LH00260:131:22L7V3LT4:3:1101:1510:1014_1:N:0:ACAGAATT+TNGCCGGT/1 83 Pocillopora_meandrina_HIv1___Sc0000008_CT_converted 1252385 42 60M = 1252385 -60 TTTGTGATATTTTTGTTAATGGTATGGAAATTATTGTTTGTAATTTTGAATTTTGAATNG 9II-II9III99I9IIIIII9I-I-9IIII9III-IIII9IIII9II-IIIIIIIIII#9 AS:i:-13 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:39T7T10G1 YS:i:-6 YT:Z:CP LH00260:131:22L7V3LT4:3:1101:1510:1014_2:N:0:ACAGAATT+TNGCCGGT/2 163 Pocillopora_meandrina_HIv1___Sc0000008_CT_converted 1252385 42 60M = 1252385 60 TTTGTGGTATTTTTGTTAATGGTATGGAAATTATTGTTTTTAATTTTTAATTTTGAATGG IIIIII-IIIIIII9IIII-IIIIIII9I-I9--II-9I9IIII9I99I-I-III-9999 AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:6A53 YS:i:-13 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from trimmed_POC-50-TP2_S14_R1_001.fastq.gz_C_to_T.fastq and trimmed_POC-50-TP2_S14_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: LH00260:131:22L7V3LT4:3:1101:1510:1014_1:N:0:ACAGAATT+TNGCCGGT/1 77 * 0 0 * * 0 0 TNATTTAAAATTTAAAATTATAAATAATAATTTTTATATTATTAATAAAAATATTATAAA 9#IIIIIIIIII-II9IIII9IIII-III9IIII9-I-I9IIIIII9I99III9II-II9 YT:Z:UP LH00260:131:22L7V3LT4:3:1101:1510:1014_2:N:0:ACAGAATT+TNGCCGGT/2 141 * 0 0 * * 0 0 TTTATAATATTTTTATTAATAATATAAAAATTATTATTTTTAATTTTTAATTTTAAATAA IIIIII-IIIIIII9IIII-IIIIIII9I-I9--II-9I9IIII9I99I-I-III-9999 YT:Z:UP >>> Writing bisulfite mapping results to trimmed_POC-50-TP2_S14_pe.bam <<< Reading in the sequence files ../output/01.00-F-Ptuh-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POC-50-TP2_S14_R1_001.fastq.gz and ../output/01.00-F-Ptuh-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POC-50-TP2_S14_R2_001.fastq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1116:23100:6393_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xfSc0000426 46955 Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1122:21684:20191_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___Sc0000027 2 Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1130:43929:5777_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___Sc0000057 3 Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1135:11819:26144_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___Sc0000019 2 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1135:11827:26158_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___Sc0000019 2 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1138:27801:1728_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xpSc0001355 1 Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1146:6470:22040_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___Sc0000034 1 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 LH00260:131:22L7V3LT4:3:1157:40498:18692_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___Sc0000027 3 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 LH00260:131:22L7V3LT4:3:1171:35157:10287_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xfSc0001231 22842 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1172:10516:1812_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___Sc0000019 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1172:10525:1826_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___Sc0000019 1 Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1178:37140:9601_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xfSc0000566 1 Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1188:43913:4320_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___Sc0000068 1 Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1193:33992:11492_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xfSc0000301 50682 Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1206:21077:13957_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___Sc0000027 1 Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1210:46252:9293_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xfSc0001231 22842 Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1211:28724:11226_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xfSc0000788 2 Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1223:35991:11562_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xfSc0000596 42627 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1224:45394:21816_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xfSc0000621 2 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1224:4609:26438_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xpSc0001355 2 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1225:6762:26382_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xfSc0000527 44088 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1225:6770:26396_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xfSc0000527 44087 Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1231:31127:20009_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___Sc0000004 14584367 Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1239:45774:21213_1:N:0:ACAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___Sc0000042 3 Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1241:42974:22782_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xfSc0000272 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1243:34372:28483_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___Sc0000019 1 Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1250:49416:28581_1:N:0:ACAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___Sc0000032 1 Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1259:35012:2695_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xfSc0000621 3 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 LH00260:131:22L7V3LT4:3:1276:21773:19925_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xfSc0000621 3 Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1290:21376:23048_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xfSc0000621 2 Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1301:12823:19504_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___Sc0000019 2 Processed 44000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1306:43055:10063_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___Sc0000019 2 Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1339:41405:23539_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___Sc0000030 2 Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 57000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1366:51544:11394_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xfSc0000488 1 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 LH00260:131:22L7V3LT4:3:1382:33320:22376_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xfSc0000272 3 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1382:7199:24393_1:N:0:ACAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xfSc0001170 1 Processed 62000000 sequence pairs so far Processed 63000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1393:41809:1574_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xfSc0001231 22818 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1393:41801:1588_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xfSc0001231 22818 Processed 64000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1402:31483:6925_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___Sc0000042 1 Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 67000000 sequence pairs so far Processed 68000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1416:43419:1644_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___Sc0000019 2 Processed 69000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1422:33482:10777_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xfSc0000621 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1422:33474:10791_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xfSc0000621 1 Processed 70000000 sequence pairs so far Processed 71000000 sequence pairs so far Processed 72000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1433:12774:11436_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xfSc0000272 3 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1433:6365:22306_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xfSc0000527 44089 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1434:3144:5749_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xfSc0000272 3 Processed 73000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1438:25835:18916_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xfSc0000566 1 Processed 74000000 sequence pairs so far Processed 75000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1447:32382:13663_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xfSc0001170 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 LH00260:131:22L7V3LT4:3:1468:40976:15260_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xfSc0000704 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1470:15267:5272_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xpSc0001337 6723 Processed 80000000 sequence pairs so far Processed 81000000 sequence pairs so far Processed 82000000 sequence pairs so far Processed 83000000 sequence pairs so far Processed 84000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1491:19199:24435_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___Sc0000012 10024529 Processed 85000000 sequence pairs so far Processed 86000000 sequence pairs so far Processed 87000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2110:35983:14826_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___Sc0000019 1 Processed 88000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2114:47110:27979_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___Sc0000042 1 Processed 89000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2117:7110:19672_1:N:0:GCAGAATT+TGACCGGT Pocillopora_meandrina_HIv1___xpSc0001355 2 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 LH00260:131:22L7V3LT4:3:2137:39632:16913_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___Sc0000030 1 Processed 94000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2140:46600:26368_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___Sc0000019 2 Processed 95000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2146:27818:27251_1:N:0:ACAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xfSc0000262 3 Processed 96000000 sequence pairs so far Processed 97000000 sequence pairs so far Processed 98000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2160:51342:5244_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___Sc0000019 1 Processed 99000000 sequence pairs so far Processed 100000000 sequence pairs so far Processed 101000000 sequence pairs so far Processed 102000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2176:23132:12809_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___Sc0000004 14584367 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2176:50953:19140_1:N:0:ACAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xfSc0000527 44128 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 Processed 109000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2215:36047:5721_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xpSc0001355 2 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2215:36056:5735_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xpSc0001355 2 Processed 110000000 sequence pairs so far Processed 111000000 sequence pairs so far Processed 112000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2229:24233:12556_1:N:0:ACAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___Sc0000019 2 Processed 113000000 sequence pairs so far 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 LH00260:131:22L7V3LT4:3:2244:14474:5300_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___Sc0000045 3 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 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2274:38977:28077_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xfSc0000885 36373 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2277:17168:17333_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xfSc0000428 1 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 LH00260:131:22L7V3LT4:3:2290:28878:10904_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xfSc0000527 44086 Processed 126000000 sequence pairs so far Processed 127000000 sequence pairs so far Processed 128000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2310:7967:1378_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xpSc0001355 1 Processed 129000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2313:23326:6085_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___Sc0000005 1 Processed 130000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2317:17727:24351_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___Sc0000045 3 Processed 131000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2321:30537:9153_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xpSc0001355 1 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2322:22938:24379_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___Sc0000019 1 Processed 132000000 sequence pairs so far Processed 133000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2332:44431:24295_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___Sc0000019 2 Processed 134000000 sequence pairs so far Processed 135000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2339:8267:14560_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xpSc0001355 1 Processed 136000000 sequence pairs so far Processed 137000000 sequence pairs so far Processed 138000000 sequence pairs so far Processed 139000000 sequence pairs so far Processed 140000000 sequence pairs so far 167114293 reads; of these: 167114293 (100.00%) were paired; of these: 121342079 (72.61%) aligned concordantly 0 times 22346846 (13.37%) aligned concordantly exactly 1 time 23425368 (14.02%) aligned concordantly >1 times 27.39% overall alignment rate Processed 141000000 sequence pairs so far Processed 142000000 sequence pairs so far Processed 143000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2379:46762:23118_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xfSc0000262 1 Processed 144000000 sequence pairs so far Processed 145000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2388:51609:6491_1:N:0:ACAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xpSc0001337 3 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2391:8097:19925_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___Sc0000019 1 Processed 146000000 sequence pairs so far Processed 147000000 sequence pairs so far Processed 148000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2407:12968:10567_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xpSc0001355 2 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2410:28182:2947_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xfSc0000262 1 Processed 149000000 sequence pairs so far 167114293 reads; of these: 167114293 (100.00%) were paired; of these: 128111273 (76.66%) aligned concordantly 0 times 19463080 (11.65%) aligned concordantly exactly 1 time 19539940 (11.69%) aligned concordantly >1 times 23.34% overall alignment rate 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 LH00260:131:22L7V3LT4:3:2424:27672:16268_1:N:0:ACAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xfSc0000092 2 Processed 153000000 sequence pairs so far Processed 154000000 sequence pairs so far Processed 155000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2442:29104:24463_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___Sc0000010 2 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2443:3687:6771_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xpSc0001355 2 Processed 156000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2446:11382:4096_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xfSc0001122 29030 167114293 reads; of these: 167114293 (100.00%) were paired; of these: 117900458 (70.55%) aligned concordantly 0 times 24455401 (14.63%) aligned concordantly exactly 1 time 24758434 (14.82%) aligned concordantly >1 times 29.45% overall alignment rate Processed 157000000 sequence pairs so far Processed 158000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2456:25309:20555_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___Sc0000045 3 Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2456:25301:20569_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___Sc0000045 3 Processed 159000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2458:9618:14602_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xfSc0001170 1 Processed 160000000 sequence pairs so far 167114293 reads; of these: 167114293 (100.00%) were paired; of these: 126906767 (75.94%) aligned concordantly 0 times 20024512 (11.98%) aligned concordantly exactly 1 time 20183014 (12.08%) aligned concordantly >1 times 24.06% overall alignment rate Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2467:43865:10315_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___xfSc0000840 37133 Processed 161000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2472:40773:4460_1:N:0:GCAGAATT+TGGCCGGT Pocillopora_meandrina_HIv1___Sc0000019 1 Processed 162000000 sequence pairs so far Processed 163000000 sequence pairs so far 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 167114293 sequences in total Successfully deleted the temporary files trimmed_POC-50-TP2_S14_R1_001.fastq.gz_C_to_T.fastq, trimmed_POC-50-TP2_S14_R1_001.fastq.gz_G_to_A.fastq, trimmed_POC-50-TP2_S14_R2_001.fastq.gz_C_to_T.fastq and trimmed_POC-50-TP2_S14_R2_001.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 167114293 Final Cytosine Methylation Report ================================= Total number of C's analysed: 3215206295 Total methylated C's in CpG context: 24480584 Total methylated C's in CHG context: 18188843 Total methylated C's in CHH context: 65242926 Total methylated C's in Unknown context: 6833414 Total unmethylated C's in CpG context: 553212268 Total unmethylated C's in CHG context: 643381408 Total unmethylated C's in CHH context: 1910700266 Total unmethylated C's in Unknown context: 35089127 C methylated in CpG context: 4.2% C methylated in CHG context: 2.7% C methylated in CHH context: 3.3% C methylated in unknown context (CN or CHN): 16.3% Bismark completed in 0d 11h 26m 2s ==================== Bismark run complete ====================