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-47-TP2_S13_R1_001.fastq.gz
../output/01.00-F-Ptuh-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POC-47-TP2_S13_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-47-TP2_S13_R1_001.fastq.gz and ../output/01.00-F-Ptuh-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POC-47-TP2_S13_R2_001.fastq.gz
Input files are in FastQ format
Writing a C -> T converted version of the input file trimmed_POC-47-TP2_S13_R1_001.fastq.gz to trimmed_POC-47-TP2_S13_R1_001.fastq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file trimmed_POC-47-TP2_S13_R1_001.fastq.gz to trimmed_POC-47-TP2_S13_R1_001.fastq.gz_G_to_A.fastq

Created C -> T as well as G -> A converted versions of the FastQ file trimmed_POC-47-TP2_S13_R1_001.fastq.gz (151987190 sequences in total)

Writing a C -> T converted version of the input file trimmed_POC-47-TP2_S13_R2_001.fastq.gz to trimmed_POC-47-TP2_S13_R2_001.fastq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file trimmed_POC-47-TP2_S13_R2_001.fastq.gz to trimmed_POC-47-TP2_S13_R2_001.fastq.gz_G_to_A.fastq

Created C -> T as well as G -> A converted versions of the FastQ file trimmed_POC-47-TP2_S13_R2_001.fastq.gz (151987190 sequences in total)

Input files are trimmed_POC-47-TP2_S13_R1_001.fastq.gz_C_to_T.fastq and trimmed_POC-47-TP2_S13_R1_001.fastq.gz_G_to_A.fastq and trimmed_POC-47-TP2_S13_R2_001.fastq.gz_C_to_T.fastq and trimmed_POC-47-TP2_S13_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-47-TP2_S13_R1_001.fastq.gz_C_to_T.fastq and trimmed_POC-47-TP2_S13_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:
LH00260:131:22L7V3LT4:3:1101:3662:1014_1:N:0:AACGTTCC+ANTACTCC/1	77	*	0	0	*	*	0	0	TNTGTAGAAAGTTATGTAGATATGTTTGAATGATGAAGTGTGAGGG	9#IIIII9-9I-IIIIIIIII9IIIIII9-I9IIIIIIII-I-9-I	YT:Z:UP
LH00260:131:22L7V3LT4:3:1101:3662:1014_2:N:0:AACGTTCC+ANTACTCC/2	141	*	0	0	*	*	0	0	CCCTCACATTTCATCATTCAAACATATCTACATAACTTTCTACAAA	IIIIIII--II-IIIIIIIIII9IIIII99III9III9IIII9II9	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from trimmed_POC-47-TP2_S13_R1_001.fastq.gz_G_to_A.fastq and trimmed_POC-47-TP2_S13_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:
LH00260:131:22L7V3LT4:3:1101:3662:1014_1:N:0:AACGTTCC+ANTACTCC/1	77	*	0	0	*	*	0	0	TNTATAAAAAACTATATAAATATATTTAAATAATAAAATATAAAAA	9#IIIII9-9I-IIIIIIIII9IIIIII9-I9IIIIIIII-I-9-I	YT:Z:UP
LH00260:131:22L7V3LT4:3:1101:3662:1014_2:N:0:AACGTTCC+ANTACTCC/2	141	*	0	0	*	*	0	0	TTTTTATGTTTTATTATTTAAATATATTTATATAGTTTTTTATAAA	IIIIIII--II-IIIIIIIIII9IIIII99III9III9IIII9II9	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from trimmed_POC-47-TP2_S13_R1_001.fastq.gz_G_to_A.fastq and trimmed_POC-47-TP2_S13_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:
LH00260:131:22L7V3LT4:3:1101:3662:1014_1:N:0:AACGTTCC+ANTACTCC/1	77	*	0	0	*	*	0	0	TNTATAAAAAACTATATAAATATATTTAAATAATAAAATATAAAAA	9#IIIII9-9I-IIIIIIIII9IIIIII9-I9IIIIIIII-I-9-I	YT:Z:UP
LH00260:131:22L7V3LT4:3:1101:3662:1014_2:N:0:AACGTTCC+ANTACTCC/2	141	*	0	0	*	*	0	0	TTTTTATGTTTTATTATTTAAATATATTTATATAGTTTTTTATAAA	IIIIIII--II-IIIIIIIIII9IIIII99III9III9IIII9II9	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from trimmed_POC-47-TP2_S13_R1_001.fastq.gz_C_to_T.fastq and trimmed_POC-47-TP2_S13_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:
LH00260:131:22L7V3LT4:3:1101:3662:1014_1:N:0:AACGTTCC+ANTACTCC/1	83	Pocillopora_meandrina_HIv1___Sc0000031_GA_converted	769095	40	46M	=	769095	-46	CCCTCACACTTCATCATTCAAACATATCTACATAACTTTCTACANA	I-9-I-IIIIIIII9I-9IIIIII9IIIIIIIII-I9-9IIIII#9	AS:i:-7	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:3A40A1	YS:i:-12	YT:Z:CP
LH00260:131:22L7V3LT4:3:1101:3662:1014_2:N:0:AACGTTCC+ANTACTCC/2	163	Pocillopora_meandrina_HIv1___Sc0000031_GA_converted	769095	40	46M	=	769095	46	CCCTCACATTTCATCATTCAAACATATCTACATAACTTTCTACAAA	IIIIIII--II-IIIIIIIIII9IIIII99III9III9IIII9II9	AS:i:-12	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:3A4C37	YS:i:-7	YT:Z:CP

>>> Writing bisulfite mapping results to trimmed_POC-47-TP2_S13_pe.bam <<<


Reading in the sequence files ../output/01.00-F-Ptuh-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POC-47-TP2_S13_R1_001.fastq.gz and ../output/01.00-F-Ptuh-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POC-47-TP2_S13_R2_001.fastq.gz
Processed 1000000 sequence pairs so far
Processed 2000000 sequence pairs so far
Processed 3000000 sequence pairs so far
Processed 4000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1122:21854:9139_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xpSc0001355	2
Processed 5000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1130:29873:12374_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___Sc0000019	1
Processed 6000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1131:16634:24925_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xpSc0001355	2
Processed 7000000 sequence pairs so far
Processed 8000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1141:35125:6337_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xpSc0001355	2
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1143:24362:12248_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xpSc0001355	2
Processed 9000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1150:19029:22432_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___Sc0000010	2
Processed 10000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1155:13543:19490_1:N:0:AACGTTCC+GGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000262	1
Processed 11000000 sequence pairs so far
Processed 12000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1162:50120:28763_1:N:0:AACGTTCC+GGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000074	2
Processed 13000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1169:35036:14027_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___Sc0000010	2
Processed 14000000 sequence pairs so far
Processed 15000000 sequence pairs so far
Processed 16000000 sequence pairs so far
Processed 17000000 sequence pairs so far
Processed 18000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1193:50484:14938_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000262	1
Processed 19000000 sequence pairs so far
Processed 20000000 sequence pairs so far
Processed 21000000 sequence pairs so far
Processed 22000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1217:40053:12038_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000885	36321
Processed 23000000 sequence pairs so far
Processed 24000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1224:39098:15708_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___Sc0000019	2
Processed 25000000 sequence pairs so far
Processed 26000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1236:17468:21577_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000262	1
Processed 27000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1239:1146:21984_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xpSc0001355	1
Processed 28000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1244:25010:23679_1:N:0:AACGTTCC+GGTACTCC	Pocillopora_meandrina_HIv1___Sc0000019	1
Processed 29000000 sequence pairs so far
Processed 30000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1255:48663:11394_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000428	2
Processed 31000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1262:51123:29688_1:N:0:AACGTTCC+NGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000272	3
Processed 32000000 sequence pairs so far
Processed 33000000 sequence pairs so far
Processed 34000000 sequence pairs so far
Processed 35000000 sequence pairs so far
Processed 36000000 sequence pairs so far
Processed 37000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1290:35513:3956_1:N:0:GACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___Sc0000019	2
Processed 38000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1301:7231:15400_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000272	3
Processed 39000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1304:30237:2891_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___Sc0000009	2
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1306:42489:12304_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000272	3
Processed 40000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1307:43314:27405_1:N:0:AACGTTCC+GGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000527	44136
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1308:26215:28175_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___Sc0000019	1
Processed 41000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1314:47636:1294_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0001231	22842
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1314:17694:24099_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000655	41337
Processed 42000000 sequence pairs so far
Processed 43000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1324:40045:23174_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000812	1
Processed 44000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1330:15809:22712_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000092	2
Processed 45000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1333:10427:22418_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000527	44116
Processed 46000000 sequence pairs so far
Processed 47000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1345:5952:3045_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___Sc0000055	121511
Processed 48000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1351:13664:17487_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___Sc0000016	9288055
Processed 49000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1357:35424:10077_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___Sc0000055	121515
Processed 50000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1361:19272:28007_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000272	3
Processed 51000000 sequence pairs so far
Processed 52000000 sequence pairs so far
Processed 53000000 sequence pairs so far
Processed 54000000 sequence pairs so far
Processed 55000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1388:46753:25374_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000272	3
Processed 56000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1392:45491:15120_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___Sc0000004	14584379
Processed 57000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1397:24565:26354_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000205	2
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1402:15946:18832_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___Sc0000076	54435
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	LH00260:131:22L7V3LT4:3:1422:25350:25051_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___Sc0000003	19417365
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1423:10168:5889_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___Sc0000019	1
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1423:10160:5903_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___Sc0000019	1
Processed 63000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1432:2610:8522_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___Sc0000004	14584367
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1432:2618:8536_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___Sc0000004	14584367
Processed 64000000 sequence pairs so far
Processed 65000000 sequence pairs so far
Processed 66000000 sequence pairs so far
Processed 67000000 sequence pairs so far
Processed 68000000 sequence pairs so far
Processed 69000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1461:12693:25107_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000205	2
Processed 70000000 sequence pairs so far
Processed 71000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1469:33207:2597_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000272	3
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1472:45451:8914_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0001179	2
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1473:28295:18244_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___Sc0000023	5766994
Processed 72000000 sequence pairs so far
Processed 73000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1483:24160:15316_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___Sc0000009	2
Processed 74000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1485:43460:5104_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000262	3
Processed 75000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:1490:44690:21549_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___Sc0000019	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	LH00260:131:22L7V3LT4:3:2113:45847:7079_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___Sc0000055	121515
Processed 80000000 sequence pairs so far
Processed 81000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:2127:39729:25990_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000704	1
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:2127:17808:27377_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000262	1
Processed 82000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:2130:46333:11170_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000596	42631
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:2133:15323:9040_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000704	1
Processed 83000000 sequence pairs so far
Processed 84000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:2143:50047:8018_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000074	1
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	LH00260:131:22L7V3LT4:3:2155:46818:10441_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___Sc0000019	2
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:2157:29711:3802_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___Sc0000004	14584379
Processed 88000000 sequence pairs so far
Processed 89000000 sequence pairs so far
Processed 90000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:2173:28465:8928_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___Sc0000063	73308
Processed 91000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:2175:10047:2765_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___Sc0000019	1
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:2175:10055:2779_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___Sc0000019	1
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:2175:27243:21437_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000272	3
Processed 92000000 sequence pairs so far
Processed 93000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:2187:9990:1826_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000205	1
Processed 94000000 sequence pairs so far
Processed 95000000 sequence pairs so far
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	LH00260:131:22L7V3LT4:3:2215:32357:13789_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000272	3
Processed 99000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:2217:29145:16885_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000428	1
Processed 100000000 sequence pairs so far
Processed 101000000 sequence pairs so far
Processed 102000000 sequence pairs so far
Processed 103000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:2240:8089:27615_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xpSc0001321	15189
Processed 104000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:2247:8056:22824_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000272	2
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	LH00260:131:22L7V3LT4:3:2270:49707:16563_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000004	334646
Processed 110000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:2274:14563:6715_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000477	45717
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:2274:35489:22320_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000272	2
Processed 111000000 sequence pairs so far
Processed 112000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:2284:43614:11506_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___Sc0000004	14584367
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:2285:26531:12640_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000527	44100
Processed 113000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:2291:46948:13411_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___Sc0000019	2
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	LH00260:131:22L7V3LT4:3:2314:46033:18356_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000272	3
Processed 118000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:2322:42295:14265_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000272	3
Processed 119000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:2327:50654:14504_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___Sc0000057	3
Processed 120000000 sequence pairs so far
Processed 121000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:2335:37852:7472_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000217	2
Processed 122000000 sequence pairs so far
Processed 123000000 sequence pairs so far
Processed 124000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:2354:12645:12052_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0001231	22875
Processed 125000000 sequence pairs so far
Processed 126000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:2364:34138:17179_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000272	3
Processed 127000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:2369:40377:4390_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___Sc0000023	5767011
Processed 128000000 sequence pairs so far
Processed 129000000 sequence pairs so far
Processed 130000000 sequence pairs so far
Processed 131000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:2386:15000:7528_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000205	1
Processed 132000000 sequence pairs so far
Processed 133000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:2396:44747:28595_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___Sc0000037	3
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:2403:10185:4012_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000725	39742
Processed 134000000 sequence pairs so far
151987190 reads; of these:
  151987190 (100.00%) were paired; of these:
    110141970 (72.47%) aligned concordantly 0 times
    20890475 (13.74%) aligned concordantly exactly 1 time
    20954745 (13.79%) aligned concordantly >1 times
27.53% overall alignment rate
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:2405:48663:9265_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___Sc0000057	3
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:2408:33312:21437_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000621	1
Processed 135000000 sequence pairs so far
151987190 reads; of these:
  151987190 (100.00%) were paired; of these:
    108147009 (71.16%) aligned concordantly 0 times
    22114789 (14.55%) aligned concordantly exactly 1 time
    21725392 (14.29%) aligned concordantly >1 times
28.84% overall alignment rate
Processed 136000000 sequence pairs so far
Processed 137000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:2422:2885:25388_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000272	3
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:2423:18746:8550_1:N:0:AACGTTCC+GGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000974	1
Processed 138000000 sequence pairs so far
Processed 139000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:2436:49205:26368_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000272	3
Processed 140000000 sequence pairs so far
Processed 141000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:2447:31548:10511_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___Sc0000019	2
Processed 142000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:2450:20551:28567_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000262	1
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:2451:51512:14251_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000527	44125
Processed 143000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:2454:41477:11758_1:N:0:GACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0001231	22837
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:2455:13867:24841_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000288	51282
Processed 144000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:2458:14498:28007_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___Sc0000063	73309
Processed 145000000 sequence pairs so far
Processed 146000000 sequence pairs so far
Processed 147000000 sequence pairs so far
Processed 148000000 sequence pairs so far
Processed 149000000 sequence pairs so far
151987190 reads; of these:
  151987190 (100.00%) were paired; of these:
    114809674 (75.54%) aligned concordantly 0 times
    18812491 (12.38%) aligned concordantly exactly 1 time
    18365025 (12.08%) aligned concordantly >1 times
24.46% overall alignment rate
151987190 reads; of these:
  151987190 (100.00%) were paired; of these:
    114070204 (75.05%) aligned concordantly 0 times
    19166257 (12.61%) aligned concordantly exactly 1 time
    18750729 (12.34%) aligned concordantly >1 times
24.95% overall alignment rate
Processed 150000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00260:131:22L7V3LT4:3:2492:24726:3746_1:N:0:AACGTTCC+AGTACTCC	Pocillopora_meandrina_HIv1___xfSc0000272	3
Processed 151000000 sequence pairs so far
Processed 151987190 sequences in total


Successfully deleted the temporary files trimmed_POC-47-TP2_S13_R1_001.fastq.gz_C_to_T.fastq, trimmed_POC-47-TP2_S13_R1_001.fastq.gz_G_to_A.fastq, trimmed_POC-47-TP2_S13_R2_001.fastq.gz_C_to_T.fastq and trimmed_POC-47-TP2_S13_R2_001.fastq.gz_G_to_A.fastq

Final Alignment report
======================
Sequence pairs analysed in total:	151987190
Final Cytosine Methylation Report
=================================
Total number of C's analysed:	3022744266

Total methylated C's in CpG context:	21446654
Total methylated C's in CHG context:	15194531
Total methylated C's in CHH context:	62636135
Total methylated C's in Unknown context:	7115726

Total unmethylated C's in CpG context:	516406005
Total unmethylated C's in CHG context:	602797818
Total unmethylated C's in CHH context:	1804263123
Total unmethylated C's in Unknown context:	35351450

C methylated in CpG context:	4.0%
C methylated in CHG context:	2.5%
C methylated in CHH context:	3.4%
C methylated in unknown context (CN or CHN):	16.8%


Bismark completed in 0d 11h 8m 24s

====================
Bismark run complete
====================