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/81M_R1.fastp-trim.fq.gz
../data/81M_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/81M_R1.fastp-trim.fq.gz and ../data/81M_R2.fastp-trim.fq.gz
Input files are in FastQ format
Writing a C -> T converted version of the input file 81M_R1.fastp-trim.fq.gz to 81M_R1.fastp-trim.fq.gz_C_to_T.fastq

Created C -> T converted version of the FastQ file 81M_R1.fastp-trim.fq.gz (90494064 sequences in total)

Writing a G -> A converted version of the input file 81M_R2.fastp-trim.fq.gz to 81M_R2.fastp-trim.fq.gz_G_to_A.fastq

Created G -> A converted version of the FastQ file 81M_R2.fastp-trim.fq.gz (90494064 sequences in total)

Input files are 81M_R1.fastp-trim.fq.gz_C_to_T.fastq and 81M_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 81M_R1.fastp-trim.fq.gz_C_to_T.fastq and 81M_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:
LH00469:254:22HGFVLT4:2:1101:1186:1014_1:N:0:GAAGGAAG+GACGTCAT/1	99	NC_086375.1_CT_converted	75644245	40	93M4I12M	=	75644225	-125	TTGTAATTATAATTAAGTTAGTTTTTTATTTTATTTTTAAATTTTTAAAAAGTAAGGGAAAGATTAATTTTGGTTTTATTTATTTTTGAATAATTTTTTTTTTTTTTTT	IIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III9IIIII9III-IIIIIII9IIIIIIIIIIIIIIIIIII	AS:i:-41	XN:i:0	XM:i:4	XO:i:1	XG:i:4	NM:i:8	MD:Z:95G2A2A0A2	YS:i:-6	YT:Z:CP
LH00469:254:22HGFVLT4:2:1101:1186:1014_2:N:0:GAAGGAAG+GACGTCAT/2	147	NC_086375.1_CT_converted	75644225	40	109M	=	75644245	125	AATGTGAAAGATTTTTTTTGTTGTAATTATAATTAAGTTAGTTTTTTATTTTATTTTTAAATTTTTAAAAAGTAAGGGAAAGATTAATTTTGGTTTTATTTATTTTTGA	IIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9I-IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-	AS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:19T89	YS:i:-41	YT:Z:CP
Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 81M_R1.fastp-trim.fq.gz_C_to_T.fastq and 81M_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:
LH00469:254:22HGFVLT4:2:1101:1186:1014_1:N:0:GAAGGAAG+GACGTCAT/1	77	*	0	0	*	*	0	0	TTGTAATTATAATTAAGTTAGTTTTTTATTTTATTTTTAAATTTTTAAAAAGTAAGGGAAAGATTAATTTTGGTTTTATTTATTTTTGAATAATTTTTTTTTTTTTTTT	IIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III9IIIII9III-IIIIIII9IIIIIIIIIIIIIIIIIII	YT:Z:UP
LH00469:254:22HGFVLT4:2:1101:1186:1014_2:N:0:GAAGGAAG+GACGTCAT/2	141	*	0	0	*	*	0	0	TCAAAAATAAATAAAACCAAAATTAATCTTTCCCTTACTTTTTAAAAATTTAAAAATAAAATAAAAAACTAACTTAATTATAATTACAACAAAAAAAATCTTTCACATT	-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII-I9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIII	YT:Z:UP

>>> Writing bisulfite mapping results to 81M_pe.bam <<<


Reading in the sequence files ../data/81M_R1.fastp-trim.fq.gz and ../data/81M_R2.fastp-trim.fq.gz
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1107:20462:2135_1:N:0:GAAGGAAG+GACGTCAT	NW_026963725.1	2
Processed 1000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1112:18431:20891_1:N:0:GAAGGAAG+GACGTCAT	NW_026963494.1	1
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1114:9464:1728_1:N:0:GAAGGAAG+GACGTCAT	NW_026963684.1	18481
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1117:34405:26382_1:N:0:GAAGGAAG+GACGTCAT	NW_026963421.1	23836
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	LH00469:254:22HGFVLT4:2:1146:9100:11352_1:N:0:GAAGGAAG+GACGTCAT	NW_026963749.1	1
Processed 5000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1149:23205:6967_1:N:0:GAAGGAAG+GACGTCAT	NW_026963353.1	20283
Processed 6000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1162:26353:10932_1:N:0:GAAGGAAG+GACGTCAT	NW_026963650.1	20965
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1164:49335:15582_1:N:0:GAAGGAAG+GACGTCAT	NW_026963725.1	2
Processed 7000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1170:11949:22390_1:N:0:GAAGGAAG+GACGTCAT	NW_026963673.1	26159
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1171:33377:17459_1:N:0:GAAGGAAG+GACGTCAT	NW_026963354.1	394789
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1172:30618:16409_1:N:0:GAAGGAAG+GACGTCAT	NW_026963801.1	31735
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1173:30342:6099_1:N:0:GAAGGAAG+GACGTCAT	NW_026963443.1	56339
Processed 8000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1180:25827:23973_1:N:0:GAAGGAAG+GACGTCAT	NW_026963309.1	1
Processed 9000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1195:21724:5749_1:N:0:GAAGGAAG+GACGTCAT	NW_026963731.1	22055
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1196:36331:27867_1:N:0:GAAGGAAG+GACGTCAT	NW_026963403.1	1
Processed 10000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1206:15874:17417_1:N:0:GAAGGAAG+GACGTCAT	NW_026963443.1	1
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1206:15890:17417_1:N:0:GAAGGAAG+GACGTCAT	NW_026963443.1	1
Processed 11000000 sequence pairs so far
Processed 12000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1219:13915:14363_1:N:0:GAAGGAAG+GACGTCAT	NW_026963667.1	2
Processed 13000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1230:38378:25219_1:N:0:GAAGGAAG+GACGTCAT	NW_026963307.1	124870
Processed 14000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1246:3290:20541_1:N:0:GAAGGAAG+GACGTCAT	NW_026963443.1	56334
Processed 15000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1253:8599:19392_1:N:0:GAAGGAAG+GACGTCAT	NW_026963442.1	1
Processed 16000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1262:24904:5819_1:N:0:GAAGGAAG+GACGTCAT	NW_026963784.1	24900
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1266:25390:25149_1:N:0:GAAGGAAG+GACGTCAT	NW_026963737.1	15360
Processed 17000000 sequence pairs so far
Processed 18000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1286:11552:18818_1:N:0:GAAGGAAG+GACGTCAT	NW_026963427.1	1
Processed 19000000 sequence pairs so far
Processed 20000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1307:37245:2247_1:N:0:GAAGGAAG+GACGTCAT	NW_026963725.1	2
Processed 21000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1319:25010:20597_1:N:0:GAAGGAAG+GACGTCAT	NW_026963554.1	23187
Processed 22000000 sequence pairs so far
Processed 23000000 sequence pairs so far
Processed 24000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1341:22218:5679_1:N:0:GAAGGAAG+GACGTCAT	NW_026963415.1	1
Processed 25000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1352:17209:28581_1:N:0:GAAGGAAG+GACGTCAT	NW_026963802.1	1
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1352:17225:28581_1:N:0:GAAGGAAG+GACGTCAT	NW_026963802.1	1
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1355:14927:23987_1:N:0:GAAGGAAG+GACGTCAT	NW_026963684.1	18489
Processed 26000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1359:24484:28091_1:N:0:GAAGGAAG+GACGTCAT	NW_026963353.1	20280
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1364:31233:20611_1:N:0:GAAGGAAG+GACGTCAT	NW_026963377.1	1
Processed 27000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1374:28238:21788_1:N:0:GAAGGAAG+GACGTCAT	NW_026963725.1	1
Processed 28000000 sequence pairs so far
Processed 29000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1394:2683:13663_1:N:0:GAAGGAAG+GACGTCAT	NW_026963743.1	1
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1397:27591:8760_1:N:0:GAAGGAAG+GACGTCAT	NW_026963741.1	1
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1397:27607:8760_1:N:0:GAAGGAAG+GACGTCAT	NW_026963741.1	1
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1397:27599:8774_1:N:0:GAAGGAAG+GACGTCAT	NW_026963741.1	1
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1398:10079:24393_1:N:0:GAAGGAAG+GACGTCAT	NW_026963477.1	2
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1398:10088:24407_1:N:0:GAAGGAAG+GACGTCAT	NW_026963477.1	2
Processed 30000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1404:30464:5104_1:N:0:GAAAGAAG+GACGTCAT	NW_026963458.1	20702
Processed 31000000 sequence pairs so far
Processed 32000000 sequence pairs so far
Processed 33000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1437:28020:19644_1:N:0:GAAGGAAG+GACGTCAT	NW_026963442.1	1
Processed 34000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1449:8364:20331_1:N:0:GAAGGAAG+GACGTCAT	NW_026963469.1	21274
Processed 35000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1457:26863:2009_1:N:0:GAAGGAAG+GACGTCAT	NW_026963619.1	23635
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1457:26879:2009_1:N:0:GAAGGAAG+GACGTCAT	NW_026963619.1	23635
Processed 36000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1471:35343:4194_1:N:0:GAAGGAAG+GATGTCAT	NW_026963577.1	20074
Processed 37000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1472:34219:2499_1:N:0:GAAGGAAG+GACGTCAT	NW_026963309.1	1
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1482:17225:1714_1:N:0:GAAGGAAG+GACGTCAT	NW_026963334.1	2
Processed 38000000 sequence pairs so far
Processed 39000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:1498:11277:1532_1:N:0:GAAGGAAG+GACGTCAT	NW_026963596.1	19277
Processed 40000000 sequence pairs so far
Processed 41000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2122:28595:11870_1:N:0:GAAGGAAG+GACGTCAT	NW_026963415.1	2
Processed 42000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2133:17484:10735_1:N:0:GAAGGAAG+GACGTCAT	NW_026963725.1	1
Processed 43000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2145:14579:8984_1:N:0:GAAGGAAG+GACGTCAT	NW_026963616.1	36417
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2145:14571:8998_1:N:0:GAAGGAAG+GACGTCAT	NW_026963616.1	36417
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2145:14563:9012_1:N:0:GAAGGAAG+GACGTCAT	NW_026963616.1	36417
Processed 44000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2147:24751:5581_1:N:0:GAAGGAAG+GACGTCAT	NW_026963585.1	2
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2151:29412:23034_1:N:0:GAAGGAAG+GACGTCAT	NW_026963673.1	26157
Processed 45000000 sequence pairs so far
Processed 46000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2174:34720:16002_1:N:0:GAAGGAAG+GACGTCAT	NW_026963663.1	21844
Processed 47000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2178:4803:4194_1:N:0:GAAGGAAG+GACGTCAT	NW_026963599.1	40053
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2178:4820:4194_1:N:0:GAAGGAAG+GACGTCAT	NW_026963599.1	40053
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2178:13640:13971_1:N:0:GAAGGAAG+GACGTCAT	NW_026963291.1	1
Processed 48000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2193:37059:7275_1:N:0:GAAGGAAG+GACGTCAT	NW_026963309.1	1
Processed 49000000 sequence pairs so far
Processed 50000000 sequence pairs so far
Processed 51000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2226:17411:9012_1:N:0:GAAGGAAG+GACGTCAT	NW_026963427.1	1
Processed 52000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2240:12774:16339_1:N:0:GAAGGAAG+GACGTCAT	NW_026963340.1	4220820
Processed 53000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2249:37010:5623_1:N:0:GAAGGAAG+GACGTCAT	NW_026963308.1	1
Processed 54000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2254:39624:2527_1:N:0:GAAGGAAG+GACGTCAT	NW_026963377.1	1
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2257:12807:2079_1:N:0:GAAGGAAG+GACGTCAT	NW_026963483.1	1
Processed 55000000 sequence pairs so far
Processed 56000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2277:30164:21283_1:N:0:GAAGGAAG+GACGTCAT	NW_026963494.1	1
Processed 57000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2297:47563:3101_1:N:0:GAAGGAAG+GACGTCAT	NW_026963536.1	19381
Processed 58000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2303:31378:26494_1:N:0:GAAGGAGG+GACGTCAT	NW_026963485.1	1
Processed 59000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2315:47239:16997_1:N:0:GAAGGAAG+GACGTCAT	NW_026963517.1	1
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	LH00469:254:22HGFVLT4:2:2343:20438:19882_1:N:0:GAAGGAAG+GACGTCAT	NW_026963510.1	2
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2343:20454:19882_1:N:0:GAAGGAAG+GACGTCAT	NW_026963510.1	2
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2343:20446:19896_1:N:0:GAAGGAAG+GACGTCAT	NW_026963510.1	2
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2343:20454:19911_1:N:0:GAAGGAAG+GACGTCAT	NW_026963510.1	2
Processed 63000000 sequence pairs so far
Processed 64000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2368:22080:4012_1:N:0:GAAGGAAG+GACGTCAT	NW_026963307.1	124890
Processed 65000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2378:9303:10805_1:N:0:GAAGGAAG+GACGTCAT	NW_026963291.1	3
Processed 66000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2386:42602:20737_1:N:0:GAAGGAAG+GACGTCAT	NW_026963442.1	1
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2386:1486:24813_1:N:0:GAAGGAAG+GACGTCAT	NW_026963316.1	1
Processed 67000000 sequence pairs so far
Processed 68000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2414:37229:27769_1:N:0:GAAGGAAG+GACGTCAT	NW_026963377.1	1
Processed 69000000 sequence pairs so far
Processed 70000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2439:6244:12150_1:N:0:GAAGGAAG+GACGTCAT	NW_026963309.1	1
Processed 71000000 sequence pairs so far
Processed 72000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2462:8866:16829_1:N:0:GAAGGAAG+GACGTCAT	NW_026963630.1	1
Processed 73000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2475:13899:3325_1:N:0:GAAGGAAG+GACGTCAT	NW_026963809.1	20346
Processed 74000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2485:10468:7304_1:N:0:GAAGGAAG+GACGTCAT	NW_026963415.1	2
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2485:50921:14377_1:N:0:GACGGAAG+GACGTCAT	NW_026963303.1	1
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2488:35829:15232_1:N:0:GAAGGCAG+GACGTCAT	NW_026963585.1	2
Chromosomal sequence could not be extracted for	LH00469:254:22HGFVLT4:2:2488:22533:26844_1:N:0:GAAGGAAG+GACGTCAT	NW_026963299.1	2
Processed 75000000 sequence pairs so far
Processed 76000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:1155:16998:22614_1:N:0:GAAGGAAG+GACGTCAT	NW_026963532.1	2
Processed 77000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:1163:41081:22586_1:N:0:GAAGGAAG+GACGTCAT	NW_026963742.1	18829
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:1195:36792:23258_1:N:0:GAAGGAAG+GACGTCAT	NW_026963443.1	1
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:1202:18495:28819_1:N:0:GAAGGAAG+GACGTCAT	NW_026963766.1	21442
Processed 78000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:1241:23205:23581_1:N:0:GAAGGAAG+GACGTCAT	NW_026963673.1	26144
Processed 79000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:1311:31087:1700_1:N:0:GAAGGAAG+GACGTCAT	NW_026963415.1	3
Processed 80000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:1368:43282:26508_1:N:0:GAAGGAAG+GACGTCAT	NW_026963308.1	1
Processed 81000000 sequence pairs so far
Processed 82000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:1472:23432:14195_1:N:0:GAAGGAAG+GACGTCAT	NW_026963771.1	24027
Processed 83000000 sequence pairs so far
Processed 84000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:2137:13988:26676_1:N:0:GAAGGAAG+GACGTCAT	NW_026963303.1	249870
Processed 85000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:2192:3217:5707_1:N:0:GAAGGAAG+GACGTCAT	NW_026963751.1	24443
Processed 86000000 sequence pairs so far
Processed 87000000 sequence pairs so far
Processed 88000000 sequence pairs so far
Processed 89000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00586:122:22HTFTLT4:7:2435:50298:20583_1:N:0:GAAGGAAG+GACGTCAT	NW_026963725.1	1
Processed 90000000 sequence pairs so far
90494064 reads; of these:
  90494064 (100.00%) were paired; of these:
    37658972 (41.61%) aligned concordantly 0 times
    17198923 (19.01%) aligned concordantly exactly 1 time
    35636169 (39.38%) aligned concordantly >1 times
58.39% overall alignment rate
90494064 reads; of these:
  90494064 (100.00%) were paired; of these:
    37641938 (41.60%) aligned concordantly 0 times
    17205461 (19.01%) aligned concordantly exactly 1 time
    35646665 (39.39%) aligned concordantly >1 times
58.40% overall alignment rate
Processed 90494064 sequences in total

Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, <IN2> line 361976256.
Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, <IN2> line 361976256.
Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, <IN2> line 361976256.
Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, <IN2> line 361976256.

Successfully deleted the temporary files 81M_R1.fastp-trim.fq.gz_C_to_T.fastq and 81M_R2.fastp-trim.fq.gz_G_to_A.fastq

Final Alignment report
======================
Sequence pairs analysed in total:	90494064
Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2214607606

Total methylated C's in CpG context:	27743548
Total methylated C's in CHG context:	3222195
Total methylated C's in CHH context:	15061143
Total methylated C's in Unknown context:	361065

Total unmethylated C's in CpG context:	235743854
Total unmethylated C's in CHG context:	354502817
Total unmethylated C's in CHH context:	1578334049
Total unmethylated C's in Unknown context:	12255909

C methylated in CpG context:	10.5%
C methylated in CHG context:	0.9%
C methylated in CHH context:	0.9%
C methylated in unknown context (CN or CHN):	2.9%


Bismark completed in 0d 6h 14m 23s

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

Unable to flush stdout: Broken pipe