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 /home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/data/	(absolute path is '/home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/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/8TB_HDD_03/sr320/github/timeseries_molecular/D-Apul/code'):
/home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1B5_R1_001.fastp-trim.fq.gz
/home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1B5_R2_001.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/8TB_HDD_03/sr320/github/timeseries_molecular/D-Apul/output/14-Apul-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/8TB_HDD_03/sr320/github/timeseries_molecular/D-Apul/code

Now reading in and storing sequence information of the genome specified in: /home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/data/

Single-core mode: setting pid to 1

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

The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1B5_R1_001.fastp-trim.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1B5_R2_001.fastp-trim.fq.gz
Input files are in FastQ format
Writing a C -> T converted version of the input file 1B5_R1_001.fastp-trim.fq.gz to 1B5_R1_001.fastp-trim.fq.gz_C_to_T.fastq

Created C -> T converted version of the FastQ file 1B5_R1_001.fastp-trim.fq.gz (40968727 sequences in total)

Writing a G -> A converted version of the input file 1B5_R2_001.fastp-trim.fq.gz to 1B5_R2_001.fastp-trim.fq.gz_G_to_A.fastq

Created G -> A converted version of the FastQ file 1B5_R2_001.fastp-trim.fq.gz (40968727 sequences in total)

Input files are 1B5_R1_001.fastp-trim.fq.gz_C_to_T.fastq and 1B5_R2_001.fastp-trim.fq.gz_G_to_A.fastq (FastQ)
Now running 2 instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/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 1B5_R1_001.fastp-trim.fq.gz_C_to_T.fastq and 1B5_R2_001.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:
LH00526:197:22KFKVLT4:3:1101:49521:1056_1:N:0:TCGGATTC+TAGTTGCG/1	77	*	0	0	*	*	0	0	AAGGGGTTTGGTTTTTTTTTTTTTTGTGTTGATTTTTTTTAATAGAGTTGTAATAATTTTTTTAATTTGGGGAAAAAATATTAGTAATAAGTTTTATAATTTTTTTTAAATGAAAATATTGGTTT	IIIIIIIIIIIIIIIIIIIIIIIII--9-I9I-9-9IIIII----9-9----9-----9-9I9-I999999999--99-9-99-9-9--99--9-9-9--999-99II99--99999-9999-99	YT:Z:UP
LH00526:197:22KFKVLT4:3:1101:49521:1056_2:N:0:TCGGATTC+TAGTTGCG/2	141	*	0	0	*	*	0	0	ATTTAATTTAATTTATATAAAATTATTATCTCCAATTAACTCCATAAAAAACTAAAATACCTATTATTATTAATAAACTTATAACCCTCAAACTAACATACATCAATATTTTCAAAATAAAAACC	IIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIII9I9IIIIIIIIIIIIIIIII-IIIIIIIIIIII9IIIIIIIIIIIIIII9II9I-III9IIIII9II9I	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1B5_R1_001.fastp-trim.fq.gz_C_to_T.fastq and 1B5_R2_001.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:
LH00526:197:22KFKVLT4:3:1101:49521:1056_1:N:0:TCGGATTC+TAGTTGCG/1	83	ptg000027l_GA_converted	3715831	40	100M1I24M	=	3715503	-452	AAACCAATATTTTCATTTAAAAAAAATTATAAAACTTATTACTAATATTTTTTCCCCAAATTAAAAAAATTATTACAACTCTATTAAAAAAAATCAACACAAAAAAAAAAAAAACCAAACCCCTT	99-9999-99999--99II99-999--9-9-9--99--9-9-99-9-99--999999999I-9I9-9-----9----9-9----IIIII9-9-I9I-9--IIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-62	XN:i:0	XM:i:9	XO:i:1	XG:i:1	NM:i:10	MD:Z:7C10T7C3T1T32C3C19T1T32	YS:i:0	YT:Z:CP
LH00526:197:22KFKVLT4:3:1101:49521:1056_2:N:0:TCGGATTC+TAGTTGCG/2	163	ptg000027l_GA_converted	3715503	40	125M	=	3715831	452	ATTTAATTTAATTTATATAAAATTATTATCTCCAATTAACTCCATAAAAAACTAAAATACCTATTATTATTAATAAACTTATAACCCTCAAACTAACATACATCAATATTTTCAAAATAAAAACC	IIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIII9I9IIIIIIIIIIIIIIIII-IIIIIIIIIIII9IIIIIIIIIIIIIII9II9I-III9IIIII9II9I	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:125	YS:i:-62	YT:Z:CP

>>> Writing bisulfite mapping results to 1B5_pe.bam <<<


Reading in the sequence files /home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1B5_R1_001.fastp-trim.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1B5_R2_001.fastp-trim.fq.gz
Processed 1000000 sequence pairs so far
Processed 2000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00526:197:22KFKVLT4:3:1172:47749:12388_1:N:0:TCGGATTC+TAGTTGCG	ptg000134l	2
Processed 3000000 sequence pairs so far
Processed 4000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00526:197:22KFKVLT4:3:1243:42246:3255_1:N:0:TCGGATTC+TAGTTGCG	ptg000033l	2625610
Processed 5000000 sequence pairs so far
Processed 6000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00526:197:22KFKVLT4:3:1313:44043:3928_1:N:0:TCGGATTC+TAGTTGCG	ptg000045l	1
Chromosomal sequence could not be extracted for	LH00526:197:22KFKVLT4:3:1313:44051:3942_1:N:0:TCGGATTC+TAGTTGCG	ptg000045l	1
Chromosomal sequence could not be extracted for	LH00526:197:22KFKVLT4:3:1320:37949:18678_1:N:0:TCGGATTC+TAGTTGCG	ptg000066l	66346
Processed 7000000 sequence pairs so far
Processed 8000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00526:197:22KFKVLT4:3:1404:24678:26494_1:N:0:TCGGATTC+TAGTTGCG	ptg000127l	1
Processed 9000000 sequence pairs so far
Processed 10000000 sequence pairs so far
Processed 11000000 sequence pairs so far
Processed 12000000 sequence pairs so far
Processed 13000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00526:197:22KFKVLT4:3:2180:45175:6085_1:N:0:TCGGATTC+TAGTTGCG	ptg000055l	50538
Processed 14000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00526:197:22KFKVLT4:3:2230:39357:11758_1:N:0:TCGGATTC+TAGTTGCG	ptg000035l	1
Chromosomal sequence could not be extracted for	LH00526:197:22KFKVLT4:3:2230:39333:11772_1:N:0:TCGGATTC+TAGTTGCG	ptg000035l	1
Chromosomal sequence could not be extracted for	LH00526:197:22KFKVLT4:3:2230:39349:11772_1:N:0:TCGGATTC+TAGTTGCG	ptg000035l	1
Chromosomal sequence could not be extracted for	LH00526:197:22KFKVLT4:3:2246:3573:17669_1:N:0:TCGGATTC+TAGTTGCG	ptg000015l	14997091
Processed 15000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00526:197:22KFKVLT4:3:2277:40798:2345_1:N:0:TCGGATTC+TAGTTGCG	ptg000033l	2625622
Chromosomal sequence could not be extracted for	LH00526:197:22KFKVLT4:3:2285:10565:24701_1:N:0:TCGGATTC+TAGTTGCG	ptg000039l	1139412
Chromosomal sequence could not be extracted for	LH00526:197:22KFKVLT4:3:2285:10573:24715_1:N:0:TCGGATTC+TAGTTGCG	ptg000039l	1139412
Processed 16000000 sequence pairs so far
Processed 17000000 sequence pairs so far
Processed 18000000 sequence pairs so far
Processed 19000000 sequence pairs so far
Processed 20000000 sequence pairs so far
Processed 21000000 sequence pairs so far
Processed 22000000 sequence pairs so far
Processed 23000000 sequence pairs so far
Processed 24000000 sequence pairs so far
Processed 25000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00526:197:22KFKVLT4:4:1253:25795:12879_1:N:0:TCGGATTC+TAGTTGCG	ptg000004l	2
Processed 26000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00526:197:22KFKVLT4:4:1296:31419:11688_1:N:0:TCGGATTC+TAGTTGCG	ptg000054l	36028
Chromosomal sequence could not be extracted for	LH00526:197:22KFKVLT4:4:1296:32544:27503_1:N:0:TCGGATTC+TAGTTGCG	ptg000187l	17982
Chromosomal sequence could not be extracted for	LH00526:197:22KFKVLT4:4:1304:24152:3928_1:N:0:TCGGATTC+TAGTTGCG	ptg000039l	1
Processed 27000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00526:197:22KFKVLT4:4:1333:6333:23314_1:N:0:TCGGATTC+TAGTTGCG	ptg000007l	12295855
Processed 28000000 sequence pairs so far
Processed 29000000 sequence pairs so far
Processed 30000000 sequence pairs so far
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	LH00526:197:22KFKVLT4:4:2144:8105:26746_1:N:0:TCGGATTC+TAGTTGCG	ptg000094l	2
Chromosomal sequence could not be extracted for	LH00526:197:22KFKVLT4:4:2144:8121:26746_1:N:0:TCGGATTC+TAGTTGCG	ptg000094l	2
Chromosomal sequence could not be extracted for	LH00526:197:22KFKVLT4:4:2144:8113:26760_1:N:0:TCGGATTC+TAGTTGCG	ptg000094l	2
Chromosomal sequence could not be extracted for	LH00526:197:22KFKVLT4:4:2155:47919:26074_1:N:0:TCGGATTC+TAGTTGCG	ptg000033l	2625597
Processed 34000000 sequence pairs so far
Processed 35000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00526:197:22KFKVLT4:4:2240:23278:25472_1:N:0:TCGGATTC+TAGTTGCG	ptg000124l	54848
Chromosomal sequence could not be extracted for	LH00526:197:22KFKVLT4:4:2242:42893:6169_1:N:0:TCGGATTC+TAGTTGCG	ptg000007l	12295855
Chromosomal sequence could not be extracted for	LH00526:197:22KFKVLT4:4:2262:16764:13439_1:N:0:TCGGATTC+TAGTTGCG	ptg000023l	45111806
Chromosomal sequence could not be extracted for	LH00526:197:22KFKVLT4:4:2263:14733:27909_1:N:0:TCGGATTC+TAGTTGCG	ptg000155l	2
Processed 36000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00526:197:22KFKVLT4:4:2283:2877:8956_1:N:0:TCGGATTC+TAGTTGCG	ptg000027l	16268248
Processed 37000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00526:197:22KFKVLT4:4:2337:27421:27068_1:N:0:TCGGATTC+TAGTTGCG	ptg000004l	1
Processed 38000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00526:197:22KFKVLT4:4:2398:23917:16296_1:N:0:TCGGATTC+TAGTTGCG	ptg000033l	2625651
Processed 39000000 sequence pairs so far
Processed 40000000 sequence pairs so far
40968727 reads; of these:
  40968727 (100.00%) were paired; of these:
    16248677 (39.66%) aligned concordantly 0 times
    8657364 (21.13%) aligned concordantly exactly 1 time
    16062686 (39.21%) aligned concordantly >1 times
60.34% overall alignment rate
40968727 reads; of these:
  40968727 (100.00%) were paired; of these:
    16261248 (39.69%) aligned concordantly 0 times
    8652643 (21.12%) aligned concordantly exactly 1 time
    16054836 (39.19%) aligned concordantly >1 times
60.31% overall alignment rate
Processed 40968727 sequences in total

Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, <IN2> line 163874908.
Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, <IN2> line 163874908.
Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, <IN2> line 163874908.
Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, <IN2> line 163874908.

Successfully deleted the temporary files 1B5_R1_001.fastp-trim.fq.gz_C_to_T.fastq and 1B5_R2_001.fastp-trim.fq.gz_G_to_A.fastq

Final Alignment report
======================
Sequence pairs analysed in total:	40968727
Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1246507827

Total methylated C's in CpG context:	24585193
Total methylated C's in CHG context:	1505658
Total methylated C's in CHH context:	6073935
Total methylated C's in Unknown context:	71753

Total unmethylated C's in CpG context:	166543446
Total unmethylated C's in CHG context:	209353758
Total unmethylated C's in CHH context:	838445837
Total unmethylated C's in Unknown context:	3286127

C methylated in CpG context:	12.9%
C methylated in CHG context:	0.7%
C methylated in CHH context:	0.7%
C methylated in unknown context (CN or CHN):	2.1%


Bismark completed in 0d 2h 52m 9s

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