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/242M_R1.fastp-trim.fq.gz
../data/242M_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/242M_R1.fastp-trim.fq.gz and ../data/242M_R2.fastp-trim.fq.gz
Input files are in FastQ format
Writing a C -> T converted version of the input file 242M_R1.fastp-trim.fq.gz to 242M_R1.fastp-trim.fq.gz_C_to_T.fastq

Created C -> T converted version of the FastQ file 242M_R1.fastp-trim.fq.gz (85898735 sequences in total)

Writing a G -> A converted version of the input file 242M_R2.fastp-trim.fq.gz to 242M_R2.fastp-trim.fq.gz_G_to_A.fastq

Created G -> A converted version of the FastQ file 242M_R2.fastp-trim.fq.gz (85898735 sequences in total)

Input files are 242M_R1.fastp-trim.fq.gz_C_to_T.fastq and 242M_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 242M_R1.fastp-trim.fq.gz_C_to_T.fastq and 242M_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:
LH00469:254:22HGFVLT4:2:1101:1251:1014_1:N:0:ATCGACAT+TGCGTAAC/1	99	NC_086375.1_CT_converted	28063303	6	131M	=	28063395	217	GGTATAGATGTGTTTATGTGATATTATGATTGTGTTTATGGAATTATAATGTGTAATTTTTTTTTTTAGATAATATAAATTTATTTTTGATGATTTTTGTATATGGTATAATAATTATATTTTTGTTTTGT	IIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II9I9IIIIIIIIIIIIIIIIIIIIIII-II9III-IIIIIIIIII9I9IIIIIIIII	AS:i:-30	XS:i:-24	XN:i:0	XM:i:5	XO:i:0	XG:i:0	NM:i:5	MD:Z:6T57A15A20G6A22	YS:i:-29	YT:Z:CP
LH00469:254:22HGFVLT4:2:1101:1251:1014_2:N:0:ATCGACAT+TGCGTAAC/2	147	NC_086375.1_CT_converted	28063395	6	70M6I55M	=	28063303	-217	ATTTTTGTAGATGGTAAAATAATTATATTTTTGTTTTGTTAGTTTTATTTAAAATTAAATGTTTAAAAAGTAATTATAATATATGATTTGTTTGTGGATTTTGTATTAGTGTGTTGTTGTAGTTATTTGTT	IIII9IIIIIIIIIIII9IIIII99IIIIIIII-IIIIIIIIII-IIII9IIIIIIIIIIII-III9IIIIII99II99III-II-IIIIIIIIIII9IIIII-9IIIIIII9I99IIIIIII-IIIIIII	AS:i:-29	XS:i:-29	XN:i:0	XM:i:1	XO:i:1	XG:i:6	NM:i:7	MD:Z:92G32	YS:i:-30	YT:Z:CP
Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 242M_R1.fastp-trim.fq.gz_C_to_T.fastq and 242M_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:
LH00469:254:22HGFVLT4:2:1101:1251:1014_1:N:0:ATCGACAT+TGCGTAAC/1	83	NC_086386.1_GA_converted	72076491	6	131M	=	72076405	-217	ACAAAACAAAAATATAATTATTATACCATATACAAAAATCATCAAAAATAAATTTATATTATCTAAAAAAAAAAATTACACATTATAATTCCATAAACACAATCATAATATCACATAAACACATCTATACC	IIIIIIIII9I9IIIIIIIIII-III9II-IIIIIIIIIIIIIIIIIIIIIII9I9II9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIII	AS:i:-30	XS:i:-30	XN:i:0	XM:i:5	XO:i:0	XG:i:0	NM:i:5	MD:Z:22T6C20T15T57A6	YS:i:-23	YT:Z:CP
LH00469:254:22HGFVLT4:2:1101:1251:1014_2:N:0:ATCGACAT+TGCGTAAC/2	163	NC_086386.1_GA_converted	72076405	6	51M6I74M	=	72076491	217	AACAAATAACTACAACAACACACTAATACAAAATCCACAAACAAATCATATATTATAATTACTTTTTAAACATTTAATTTTAAATAAAACTAACAAAACAAAAATATAATTATTTTACCATCTACAAAAAT	IIIIIII-IIIIIII99I9IIIIIII9-IIIII9IIIIIIIIIII-II-III99II99IIIIII9III-IIIIIIIIIIII9IIII-IIIIIIIIII-IIIIIIII99IIIII9IIIIIIIIIIII9IIII	AS:i:-23	XS:i:-29	XN:i:0	XM:i:0	XO:i:1	XG:i:6	NM:i:6	MD:Z:125	YS:i:-30	YT:Z:CP

>>> Writing bisulfite mapping results to 242M_pe.bam <<<


Reading in the sequence files ../data/242M_R1.fastp-trim.fq.gz and ../data/242M_R2.fastp-trim.fq.gz
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1103:24370:1532_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963469.1	21270
Processed 1000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1117:47781:27909_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963802.1	1
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1120:26669:29044_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963673.1	26158
Processed 2000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1131:7506:26158_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963415.1	2
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1131:7514:26172_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963415.1	2
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1132:9780:28049_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963784.1	2
Processed 3000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1139:11399:12977_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963687.1	26523
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1145:3719:9489_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963291.1	1
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1145:27421:26760_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963415.1	3
Processed 4000000 sequence pairs so far
Processed 5000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1163:23909:28329_1:N:0:ATCGCAAT+TGCGTAAC	NW_026963795.1	20649
Processed 6000000 sequence pairs so far
Processed 7000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1192:21716:12486_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963362.1	2
Processed 8000000 sequence pairs so far
Processed 9000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1212:7530:26172_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963667.1	28289
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1214:20122:28946_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963619.1	23636
Processed 10000000 sequence pairs so far
Processed 11000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1242:21182:16325_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963291.1	2
Processed 12000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1257:34130:12795_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963312.1	1
Processed 13000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1265:24030:19602_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963415.1	1
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1268:3460:14616_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963677.1	25109
Processed 14000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1272:51609:28735_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963390.1	1
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1276:5524:7318_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963612.1	1
Processed 15000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1284:36404:20177_1:N:0:ATCGCAAT+TGCGTAAC	NW_026963415.1	1
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1294:39462:19532_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963422.1	18055
Processed 16000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1304:49262:18146_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963415.1	2
Processed 17000000 sequence pairs so far
Processed 18000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1325:32090:17809_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963775.1	1
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1329:17621:9181_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963418.1	3
Processed 19000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1340:21813:17809_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963415.1	3
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1340:21684:19014_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963706.1	1
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1343:28141:29632_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963784.1	2
Processed 20000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1350:4463:23020_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963741.1	1
Processed 21000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1362:46867:18958_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963634.1	2
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1364:33798:14097_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963415.1	3
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1365:48056:10091_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963299.1	2
Processed 22000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1378:46503:6953_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963784.1	2
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1383:11844:17837_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963784.1	2
Processed 23000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1394:28562:12711_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963501.1	19456
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1394:10395:15050_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963415.1	1
Processed 24000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1406:12831:20807_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963418.1	3
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1410:36201:17305_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963740.1	2
Processed 25000000 sequence pairs so far
Processed 26000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1428:21004:21199_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963537.1	3
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1431:24063:18258_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963293.1	1
Processed 27000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1437:24030:14532_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963595.1	1
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1439:9060:10946_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963794.1	13148
Processed 28000000 sequence pairs so far
Processed 29000000 sequence pairs so far
Processed 30000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1477:34211:14840_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963474.1	24584
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1481:29736:24071_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963564.1	19022
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1482:13859:22502_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963415.1	2
Processed 31000000 sequence pairs so far
Processed 32000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2112:9974:18272_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963784.1	2
Processed 33000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2115:4043:11366_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963305.1	1249870
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2119:40142:8270_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963784.1	2
Processed 34000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2130:22461:25177_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963307.1	124881
Processed 35000000 sequence pairs so far
Processed 36000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2151:30626:16254_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963784.1	2
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2159:32139:24001_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963809.1	20337
Processed 37000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2167:2885:13957_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963360.1	21745
Processed 38000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2175:46923:25976_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963333.1	249875
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2181:33256:18146_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963791.1	1
Processed 39000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2196:13082:21297_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963703.1	26910
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2198:23343:14826_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963705.1	1
Processed 40000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2212:36460:13215_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963464.1	1
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2212:25843:14447_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963415.1	3
Processed 41000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2228:50225:13033_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963564.1	19023
Processed 42000000 sequence pairs so far
Processed 43000000 sequence pairs so far
Processed 44000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2257:20300:24575_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963415.1	2
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2265:49796:25318_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963775.1	1
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2265:49812:25318_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963775.1	1
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2265:49788:25332_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963775.1	1
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2265:49804:25332_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963775.1	1
Processed 45000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2273:32341:2667_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963312.1	2
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2276:16092:22054_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963415.1	3
Processed 46000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2283:51447:23104_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963564.1	19050
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2287:27729:25360_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963415.1	1
Processed 47000000 sequence pairs so far
Processed 48000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2311:21797:21031_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963794.1	13155
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2312:23124:17781_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963359.1	23038
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2313:36080:6785_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963333.1	249889
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2313:36088:6799_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963333.1	249889
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2313:38556:26620_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963415.1	3
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2316:37132:12500_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963394.1	27832
Processed 49000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2325:4714:26676_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963488.1	1
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2336:19701:6757_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963728.1	1
Processed 50000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2338:1065:15624_1:N:0:NTCGCCAT+NGCGTAAC	NW_026963581.1	2
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2340:25155:7458_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963784.1	2
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2340:25147:7472_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963784.1	2
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2340:10444:21774_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963308.1	1
Processed 51000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2362:48178:27026_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963415.1	1
Processed 52000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2371:39212:23188_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963619.1	2
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2375:4828:7233_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963333.1	249878
Processed 53000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2383:21473:1728_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963741.1	2
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2383:21473:1756_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963741.1	2
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2387:32778:2891_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963415.1	3
Processed 54000000 sequence pairs so far
Processed 55000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2416:6219:10483_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963784.1	2
Processed 56000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2423:12952:29170_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963422.1	18043
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2428:15032:11338_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963581.1	2
Processed 57000000 sequence pairs so far
Processed 58000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2453:23100:2415_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963316.1	1
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2455:22517:28301_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963415.1	3
Processed 59000000 sequence pairs so far
Processed 60000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2482:47490:15834_1:N:0:ATCTCCAT+TGCGTAAC	NW_026963680.1	1
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2489:20219:19728_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963415.1	3
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2490:2489:22068_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963315.1	4066330
Processed 61000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2493:14684:18692_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963415.1	1
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2495:49383:22726_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963705.1	1
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2496:24484:2009_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963784.1	3
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2497:42732:16395_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963388.1	30181
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:1104:46608:6575_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963425.1	2
Processed 62000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:1115:38232:29478_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963413.1	32137
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:1129:37812:16339_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963720.1	20503
Processed 63000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:1175:50605:25878_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963333.1	249896
Processed 64000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:1185:48275:1784_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963415.1	2
Processed 65000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:1230:49707:18132_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963389.1	32298
Processed 66000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:1257:39373:18286_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963743.1	1
Processed 67000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:1281:32608:9433_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963307.1	124869
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:1292:6122:12388_1:N:0:ATCGCCAT+TGCGTAAC	NC_086380.1	80675432
Processed 68000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:1311:18633:17963_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963581.1	1
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	LH00586:122:22HTFTLT4:7:1404:31686:13999_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963642.1	22042
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:1426:3096:6449_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963667.1	28272
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:1430:49545:8830_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963378.1	2
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:1431:29315:24519_1:N:0:ATCGCCAT+TGCGTAAC	NC_086385.1	3
Processed 72000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:1449:46940:27068_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963308.1	1
Processed 73000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:1474:1218:2079_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963415.1	2
Processed 74000000 sequence pairs so far
Processed 75000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:2164:38629:16773_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963415.1	1
Processed 76000000 sequence pairs so far
Processed 77000000 sequence pairs so far
Processed 78000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:2257:45572:26046_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963550.1	42768
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:2265:30310:16100_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963784.1	2
Processed 79000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:2276:31427:12570_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963581.1	2
Processed 80000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:2308:8218:14756_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963316.1	1
Processed 81000000 sequence pairs so far
Processed 82000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:2385:32519:26144_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963474.1	24594
Processed 83000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:2411:14902:29324_1:N:0:ATCGCCAT+TGCGTAAC	NW_026963794.1	13147
Processed 84000000 sequence pairs so far
Processed 85000000 sequence pairs so far
85898735 reads; of these:
  85898735 (100.00%) were paired; of these:
    29318608 (34.13%) aligned concordantly 0 times
    13796359 (16.06%) aligned concordantly exactly 1 time
    42783768 (49.81%) aligned concordantly >1 times
65.87% overall alignment rate
85898735 reads; of these:
  85898735 (100.00%) were paired; of these:
    29334320 (34.15%) aligned concordantly 0 times
    13791041 (16.05%) aligned concordantly exactly 1 time
    42773374 (49.80%) aligned concordantly >1 times
65.85% overall alignment rate
Processed 85898735 sequences in total

Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, <IN2> line 343594940.
Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, <IN2> line 343594940.
Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, <IN2> line 343594940.
Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, <IN2> line 343594940.

Successfully deleted the temporary files 242M_R1.fastp-trim.fq.gz_C_to_T.fastq and 242M_R2.fastp-trim.fq.gz_G_to_A.fastq

Final Alignment report
======================
Sequence pairs analysed in total:	85898735
Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2227176564

Total methylated C's in CpG context:	36903344
Total methylated C's in CHG context:	4027754
Total methylated C's in CHH context:	17623440
Total methylated C's in Unknown context:	482362

Total unmethylated C's in CpG context:	265741877
Total unmethylated C's in CHG context:	374199508
Total unmethylated C's in CHH context:	1528680641
Total unmethylated C's in Unknown context:	12375493

C methylated in CpG context:	12.2%
C methylated in CHG context:	1.1%
C methylated in CHH context:	1.1%
C methylated in unknown context (CN or CHN):	3.8%


Bismark completed in 0d 5h 58m 58s

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

Unable to flush stdout: Broken pipe