Bowtie 2 seems to be working fine (tested command '/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2 --version' [2.4.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools found here: '/usr/bin/samtools'
Reference genome folder provided is ../data/	(absolute path is '/home/shared/16TB_HDD_01/sr320/github/project-mytilus-methylation/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 '/home/shared/16TB_HDD_01/sr320/github/project-mytilus-methylation/code'):
../data/69M_R1.fastp-trim.fq.gz
../data/69M_R2.fastp-trim.fq.gz
Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!)
Output will be written into the directory: /home/shared/16TB_HDD_01/sr320/github/project-mytilus-methylation/output/01.2-bismark/
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: /home/shared/16TB_HDD_01/sr320/github/project-mytilus-methylation/code

Now reading in and storing sequence information of the genome specified in: /home/shared/16TB_HDD_01/sr320/github/project-mytilus-methylation/data/

Single-core mode: setting pid to 1

Paired-end alignments will be performed
=======================================

The provided filenames for paired-end alignments are ../data/69M_R1.fastp-trim.fq.gz and ../data/69M_R2.fastp-trim.fq.gz
Input files are in FastQ format
Writing a C -> T converted version of the input file 69M_R1.fastp-trim.fq.gz to 69M_R1.fastp-trim.fq.gz_C_to_T.fastq

Created C -> T converted version of the FastQ file 69M_R1.fastp-trim.fq.gz (93353347 sequences in total)

Writing a G -> A converted version of the input file 69M_R2.fastp-trim.fq.gz to 69M_R2.fastp-trim.fq.gz_G_to_A.fastq

Created G -> A converted version of the FastQ file 69M_R2.fastp-trim.fq.gz (93353347 sequences in total)

Input files are 69M_R1.fastp-trim.fq.gz_C_to_T.fastq and 69M_R2.fastp-trim.fq.gz_G_to_A.fastq (FastQ)
Now running 2 instances of Bowtie 2 against the bisulfite genome of /home/shared/16TB_HDD_01/sr320/github/project-mytilus-methylation/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 69M_R1.fastp-trim.fq.gz_C_to_T.fastq and 69M_R2.fastp-trim.fq.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:
LH00469:254:22HGFVLT4:2:1101:3646:1014_1:N:0:GTGAAGTG+GAGCAATC/1	99	NC_086373.1_CT_converted	93602713	21	131M	=	93602697	-147	TTTGTAGTTGAGTAATTTGTGATAAAATTATGTTATATTTGAGAAAATTATTAAAAAGATTTTATTTATATATTTTGTTGTTATATTGGGATAATTGTAATTGTAGTTATGATTATTTTTTTAATTTTTTT	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-18	XS:i:-74	XN:i:0	XM:i:3	XO:i:0	XG:i:0	NM:i:3	MD:Z:125A2A0G1	YS:i:0	YT:Z:CP
LH00469:254:22HGFVLT4:2:1101:3646:1014_2:N:0:GTGAAGTG+GAGCAATC/2	147	NC_086373.1_CT_converted	93602697	21	131M	=	93602713	147	AATGGTATAGAAAAATTTTGTAGTTGAGTAATTTGTGATAAAATTATGTTATATTTGAGAAAATTATTAAAAAGATTTTATTTATATATTTTGTTGTTATATTGGGATAATTGTAATTGTAGTTATGATTA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:-56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:131	YS:i:-18	YT:Z:CP
Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 69M_R1.fastp-trim.fq.gz_C_to_T.fastq and 69M_R2.fastp-trim.fq.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:
LH00469:254:22HGFVLT4:2:1101:3646:1014_1:N:0:GTGAAGTG+GAGCAATC/1	83	NC_086385.1_GA_converted	33713748	2	88M1D43M	=	33713764	148	AAAAAAATTAAAAAAATAATCATAACTACAATTACAATTATCCCAATATAACAACAAAATATATAAATAAAATCTTTTTAATAATTTTCTCAAATATAACATAATTTTATCACAAATTACTCAACTACAAA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-68	XS:i:-68	XN:i:0	XM:i:10	XO:i:1	XG:i:1	NM:i:11	MD:Z:1C0T2T14A36C1A17A0C3C5^A15T27	YS:i:-50	YT:Z:CP
LH00469:254:22HGFVLT4:2:1101:3646:1014_2:N:0:GTGAAGTG+GAGCAATC/2	163	NC_086385.1_GA_converted	33713764	2	72M1D59M	=	33713748	-148	TAATCATAACTACAATTACAATTATCCCAATATAACAACAAAATATATAAATAAAATCTTTTTAATAATTTTCTCAAATATAACATAATTTTATCACAAATTACTCAACTACAAAATTTTTCTATACCATT	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-50	XS:i:-62	XN:i:0	XM:i:7	XO:i:1	XG:i:1	NM:i:8	MD:Z:4A36C1A17A0C3C5^A15T43	YS:i:-68	YT:Z:CP

>>> Writing bisulfite mapping results to 69M_pe.bam <<<


Reading in the sequence files ../data/69M_R1.fastp-trim.fq.gz and ../data/69M_R2.fastp-trim.fq.gz
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1102:48599:22740_1:N:0:GTGAAGTG+GAGCAATC	NW_026963727.1	22276
Processed 1000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1112:48348:24911_1:N:0:GTGAAGTG+GAGCAATC	NW_026963404.1	1
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1112:48364:24911_1:N:0:GTGAAGTG+GAGCAATC	NW_026963404.1	1
Processed 2000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1123:20591:15722_1:N:0:GTGAAGTG+GAGCAATC	NW_026963335.1	1
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1123:20607:15722_1:N:0:GTGAAGTG+GAGCAATC	NW_026963335.1	1
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1126:4771:1644_1:N:0:GTGAAGTG+GAGCAATC	NW_026963732.1	2
Processed 3000000 sequence pairs so far
Processed 4000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1141:12442:14588_1:N:0:GTGAAGTG+GAGCAATC	NW_026963675.1	2
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1142:32535:2415_1:N:0:GTGAAGTG+GAGCAATC	NW_026963443.1	56349
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1142:32511:2429_1:N:0:GTGACGTG+GAGCAATC	NW_026963443.1	56349
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1148:13948:17221_1:N:0:GTGAAGTG+GAGCAATC	NW_026963394.1	27853
Processed 5000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1155:26167:5651_1:N:0:GTGAAGTG+GAGCAATC	NW_026963308.1	2
Processed 6000000 sequence pairs so far
Processed 7000000 sequence pairs so far
Processed 8000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1179:9974:1294_1:N:0:GTGGAGTG+GAGCAATC	NW_026963667.1	2
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1181:3444:21591_1:N:0:GTGAAGTG+GAGCAATC	NW_026963377.1	2
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1181:42303:27531_1:N:0:GTGAAGTG+GAGCAATC	NW_026963319.1	249875
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1183:3994:12234_1:N:0:GTGAAGTG+GAGCAATC	NW_026963404.1	1
Processed 9000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1190:11916:25780_1:N:0:GTGAAGTG+GAGCAATC	NW_026963415.1	2
Processed 10000000 sequence pairs so far
Processed 11000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1210:25099:13803_1:N:0:GTGAAGTG+GAGCAATC	NW_026963640.1	1
Processed 12000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1221:17953:1462_1:N:0:GTGAAGTG+GAGCAATC	NW_026963765.1	1
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1223:23585:25388_1:N:0:GTGAAGTG+GAGCAATC	NW_026963415.1	1
Processed 13000000 sequence pairs so far
Processed 14000000 sequence pairs so far
Processed 15000000 sequence pairs so far
Processed 16000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1266:12645:17907_1:N:0:GTGAAGTG+GAGCAATC	NW_026963347.1	1227476
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1267:46632:4740_1:N:0:GTGAAGTG+GAGCAATC	NW_026963404.1	1
Processed 17000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1271:42578:5314_1:N:0:GTGAAGTG+GAGCAATC	NW_026963677.1	25109
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1271:27785:11534_1:N:0:GTGAAGTG+GAGCAATC	NW_026963731.1	22037
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1271:35942:19294_1:N:0:GTGAAGTG+GAGCAATC	NC_007687.1	18557
Processed 18000000 sequence pairs so far
Processed 19000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1291:5273:24085_1:N:0:GTGAAGTG+GAGCCATC	NW_026963443.1	1
Processed 20000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1304:48331:3872_1:N:0:GTGAAGTG+GAGCAATC	NW_026963415.1	1
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1305:13397:21003_1:N:0:GTGAAGTG+GAGCAATC	NW_026963526.1	17957
Processed 21000000 sequence pairs so far
Processed 22000000 sequence pairs so far
Processed 23000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1335:11018:17137_1:N:0:GTGAAGTG+GAGCAATC	NW_026963501.1	19446
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1338:50435:28133_1:N:0:GTGAAGTG+GAGCAATC	NW_026963789.1	2
Processed 24000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1349:1696:16240_1:N:0:GTGAAGTG+GAGCAATC	NW_026963677.1	25112
Processed 25000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1357:15169:19981_1:N:0:GTGAAGTG+GAGCAATC	NW_026963749.1	18268
Processed 26000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1360:8016:26396_1:N:0:GTGAAGTG+GAGCAATC	NW_026963303.1	249869
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1368:12612:21409_1:N:0:GTGAAGTG+GAGCAATC	NW_026963443.1	2
Processed 27000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1377:16294:2065_1:N:0:GCGAAGTG+GAGCAATC	NW_026963341.1	1
Processed 28000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1387:38095:13215_1:N:0:GTGAAGTG+GAGCAATC	NW_026963291.1	2
Processed 29000000 sequence pairs so far
Processed 30000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1413:45596:3872_1:N:0:GTGAAGTG+GAGCAATC	NW_026963769.1	1
Processed 31000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1414:49788:7205_1:N:0:GTGAAGTG+GAGCAATC	NW_026963660.1	48574
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1414:33701:29142_1:N:0:GTGAAGTG+GAGCAATC	NW_026963415.1	1
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1417:4253:15120_1:N:0:GTGAAGTG+GAGCAATC	NW_026963667.1	1
Processed 32000000 sequence pairs so far
Processed 33000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1442:18374:28357_1:N:0:GTGAAGTG+GAGCAATC	NW_026963415.1	2
Processed 34000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1445:4763:7626_1:N:0:GTGAAGTG+GAGCAATC	NW_026963335.1	1
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1449:27761:7458_1:N:0:GTGAAGTG+GAGCAATC	NW_026963612.1	1
Processed 35000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1455:52191:17837_1:N:0:GTGAAGTG+GAGCAATC	NW_026963684.1	18479
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1461:29412:12332_1:N:0:GTGAAGTG+GAGCAATC	NW_026963765.1	1
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1461:22979:13131_1:N:0:GTGAAGTG+GAGCAATC	NW_026963680.1	1
Processed 36000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1466:39292:14279_1:N:0:GTGAAGTG+GAGCAATC	NW_026963560.1	2
Processed 37000000 sequence pairs so far
Processed 38000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1492:10427:15666_1:N:0:GTGAAGTG+GAGCAATC	NW_026963377.1	2
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	LH00469:254:22HGFVLT4:2:2121:17201:14475_1:N:0:GTGAAGTG+GAGCAATC	NW_026963415.1	1
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2126:14028:12767_1:N:0:GTGAAGTG+GAGCAATC	NW_026963418.1	3
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2127:15704:2583_1:N:0:GTGAAGTG+GAGCAATC	NW_026963794.1	13157
Processed 42000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2135:15736:4824_1:N:0:GTGAAGTG+GAGCAATC	NW_026963415.1	1
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2135:26223:25836_1:N:0:GTGAAGTG+GAGCAATC	NW_026963425.1	1
Processed 43000000 sequence pairs so far
Processed 44000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2157:8461:20527_1:N:0:GTGAAGTG+GAGCAATC	NW_026963480.1	2
Processed 45000000 sequence pairs so far
Processed 46000000 sequence pairs so far
Processed 47000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2183:5904:3381_1:N:0:GTGAAGTG+GAGCAATC	NW_026963598.1	29339
Processed 48000000 sequence pairs so far
Processed 49000000 sequence pairs so far
Processed 50000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2223:40741:11912_1:N:0:GTGAAGTG+GAGCAATC	NW_026963443.1	2
Processed 51000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2231:30917:25135_1:N:0:GTGAAGTG+GAGCAATC	NW_026963680.1	23023
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2237:30933:4964_1:N:0:GTGAAGTG+GAGCAATC	NW_026963294.1	5965271
Processed 52000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2246:30132:5370_1:N:0:GTGAAGTG+GAGCAATC	NC_086374.1	103707519
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2246:30124:5384_1:N:0:GTGAAGTG+GAGCAATC	NC_086374.1	103707519
Processed 53000000 sequence pairs so far
Processed 54000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2262:1445:13369_1:N:0:GTGAAGTG+GAGCAATC	NW_026963667.1	3
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2267:24378:14181_1:N:0:GTGAAGTG+GAGCAATC	NW_026963347.1	1227479
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	LH00469:254:22HGFVLT4:2:2298:48566:12907_1:N:0:GTGAAGTG+GAGCAATC	NW_026963404.1	1
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2304:7417:4572_1:N:0:GTGAAGTG+GAGCAATC	NW_026963640.1	24365
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2305:7943:12430_1:N:0:GTGAAGTG+GAGCACTC	NW_026963682.1	27388
Processed 58000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2310:9675:26186_1:N:0:GTGAAGTG+GAGCAATC	NW_026963308.1	1
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2315:20721:21297_1:N:0:GTGAAGTG+GAGCAATC	NW_026963413.1	2
Processed 59000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2319:22865:14475_1:N:0:GTGAAGTG+GAGCAATC	NW_026963393.1	1
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2323:51528:13775_1:N:0:GTGAAGTG+GAGCAATC	NC_086384.1	60198009
Processed 60000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2329:45766:18818_1:N:0:GTGAAGTG+GAGCAATC	NW_026963688.1	1
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2333:40741:4908_1:N:0:GTGAAGTG+GAGCAATC	NC_086384.1	60198008
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2333:8582:11576_1:N:0:GTGAAGTG+GAGCAATC	NW_026963738.1	23709
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2336:38815:12612_1:N:0:GTGAAGTG+GAGCAATC	NW_026963388.1	1
Processed 61000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2345:46066:24155_1:N:0:GTGAAGTG+GAGCAATC	NW_026963692.1	27304
Processed 62000000 sequence pairs so far
Processed 63000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2371:8801:18118_1:N:0:GTGAAGTG+GAGCAATC	NW_026963680.1	2
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2371:8793:18132_1:N:0:GTGAAGTG+GAGCAATC	NW_026963680.1	2
Processed 64000000 sequence pairs so far
Processed 65000000 sequence pairs so far
Processed 66000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2397:2983:6869_1:N:0:GTGAAGTG+GAGCAATC	NW_026963687.1	1
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2398:35295:25402_1:N:0:GTGAAGTG+GAGCAATC	NW_026963415.1	2
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2406:21368:28497_1:N:0:GTGAAGTG+GAGCAATC	NW_026963455.1	21332
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	LH00469:254:22HGFVLT4:2:2434:4771:25093_1:N:0:GTGAAGTG+GAGCAATC	NW_026963307.1	124890
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2434:4787:25093_1:N:0:GTGAAGTG+GAGCAATC	NW_026963307.1	124890
Processed 70000000 sequence pairs so far
Processed 71000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2461:13948:5651_1:N:0:GTGAAGTG+GAGCAATC	NW_026963667.1	1
Processed 72000000 sequence pairs so far
Processed 73000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2479:41744:6841_1:N:0:GTGAAGTG+GAGCAATC	NW_026963319.1	249882
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2479:41761:6841_1:N:0:GTGAAGTG+GAGCAATC	NW_026963319.1	249882
Processed 74000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2492:42497:18146_1:N:0:GTGAAGTG+GAGCAATC	NW_026963731.1	22053
Processed 75000000 sequence pairs so far
Processed 76000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:1158:10630:8116_1:N:0:GTGAAGTG+GAGCAATC	NW_026963664.1	24145
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:1179:26507:26634_1:N:0:GTGAAGTG+GAGCAATC	NW_026963501.1	19448
Processed 77000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:1192:37366:11114_1:N:0:GTGAAGTG+GAGCAATC	NW_026963482.1	3
Processed 78000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:1234:16731:1812_1:N:0:GTGAAGTG+GAGCAATC	NW_026963359.1	23031
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:1235:20130:21143_1:N:0:GTGAAGTG+GAGCAATC	NW_026963303.1	2
Processed 79000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:1279:9659:21760_1:N:0:GTGAAGTG+GAGCAATC	NW_026963378.1	1
Processed 80000000 sequence pairs so far
Processed 81000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:1361:13430:22684_1:N:0:GTGAAGTG+GAGCAATC	NW_026963415.1	1
Processed 82000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:1432:6341:2933_1:N:0:GTGAAGTG+GAGCAATC	NW_026963293.1	1
Processed 83000000 sequence pairs so far
Processed 84000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:2106:6616:28175_1:N:0:ATGAAGTG+GAGCAATC	NW_026963443.1	56343
Processed 85000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:2137:38313:29478_1:N:0:GTGAAGTG+GAGCAATC	NW_026963622.1	25212
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:2145:26749:12654_1:N:0:GTGAAGTG+GAGCAATC	NW_026963711.1	1
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:2162:13543:10889_1:N:0:GTGAAGTG+GAGCAATC	NW_026963667.1	1
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:2166:27348:24813_1:N:0:GTGAAGTG+GAGCAATC	NW_026963488.1	21444
Processed 86000000 sequence pairs so far
Processed 87000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:2227:26491:18202_1:N:0:GTGAAGTG+GAGCAATC	NW_026963415.1	3
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:2238:51852:4810_1:N:0:GTGAAGTG+GAGCAATC	NW_026963684.1	18500
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:2239:23068:1630_1:N:0:GTGAAGTG+GAGCAATC	NW_026963415.1	1
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:2243:35206:25864_1:N:0:GTGAAGTG+GAGCAATC	NW_026963415.1	3
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	LH00586:122:22HTFTLT4:7:2373:10071:23398_1:N:0:GTGAAGTG+GAGCAATC	NW_026963415.1	1
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:2375:33895:2219_1:N:0:GTGAAGTG+GAGCAATC	NW_026963308.1	1
Processed 91000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:2406:23432:9825_1:N:0:GTGAAGTG+GAGCAATC	NW_026963415.1	1
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:2409:44787:28021_1:N:0:GTGAAGTG+GAGCAATC	NW_026963415.1	1
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:2415:46308:2863_1:N:0:GTGAAGTG+GAGCAATC	NW_026963440.1	1
Processed 92000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:2449:42837:26886_1:N:0:GTGAAGTG+GAGCAATC	NW_026963308.1	2
Processed 93000000 sequence pairs so far
93353347 reads; of these:
  93353347 (100.00%) were paired; of these:
    35463608 (37.99%) aligned concordantly 0 times
    16180270 (17.33%) aligned concordantly exactly 1 time
    41709469 (44.68%) aligned concordantly >1 times
62.01% overall alignment rate
93353347 reads; of these:
  93353347 (100.00%) were paired; of these:
    35451501 (37.98%) aligned concordantly 0 times
    16176946 (17.33%) aligned concordantly exactly 1 time
    41724900 (44.70%) aligned concordantly >1 times
62.02% overall alignment rate
Processed 93353347 sequences in total

Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, <IN2> line 373413388.
Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, <IN2> line 373413388.
Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, <IN2> line 373413388.
Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, <IN2> line 373413388.

Successfully deleted the temporary files 69M_R1.fastp-trim.fq.gz_C_to_T.fastq and 69M_R2.fastp-trim.fq.gz_G_to_A.fastq

Final Alignment report
======================
Sequence pairs analysed in total:	93353347
Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2302063801

Total methylated C's in CpG context:	34544232
Total methylated C's in CHG context:	3654003
Total methylated C's in CHH context:	16549176
Total methylated C's in Unknown context:	437157

Total unmethylated C's in CpG context:	253318940
Total unmethylated C's in CHG context:	372392432
Total unmethylated C's in CHH context:	1621605018
Total unmethylated C's in Unknown context:	12747802

C methylated in CpG context:	12.0%
C methylated in CHG context:	1.0%
C methylated in CHH context:	1.0%
C methylated in unknown context (CN or CHN):	3.3%


Bismark completed in 0d 6h 22m 33s

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

Unable to flush stdout: Broken pipe