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/1H11_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/1H11_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/1H11_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/1H11_R2_001.fastp-trim.fq.gz
Input files are in FastQ format
Writing a C -> T converted version of the input file 1H11_R1_001.fastp-trim.fq.gz to 1H11_R1_001.fastp-trim.fq.gz_C_to_T.fastq

Created C -> T converted version of the FastQ file 1H11_R1_001.fastp-trim.fq.gz (37970452 sequences in total)

Writing a G -> A converted version of the input file 1H11_R2_001.fastp-trim.fq.gz to 1H11_R2_001.fastp-trim.fq.gz_G_to_A.fastq

Created G -> A converted version of the FastQ file 1H11_R2_001.fastp-trim.fq.gz (37970452 sequences in total)

Input files are 1H11_R1_001.fastp-trim.fq.gz_C_to_T.fastq and 1H11_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 1H11_R1_001.fastp-trim.fq.gz_C_to_T.fastq and 1H11_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:
LH00526:197:22KFKVLT4:3:1101:50379:1056_1:N:0:GATAGCCA+CTGTGTTG/1	99	ntLink_8_CT_converted	15152789	42	92M	=	15152764	-117	ATTTGTTGGAAGTAGGTTTATATTGGAATTGAATATGGTGTGTTGTAAGAGATAAAATGTAGTAAGGTAATAATATAAAAAATTTAATATTA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:92	YS:i:0	YT:Z:CP
LH00526:197:22KFKVLT4:3:1101:50379:1056_2:N:0:GATAGCCA+CTGTGTTG/2	147	ntLink_8_CT_converted	15152764	42	92M	=	15152789	117	AATAATTTGTGAAAGAAGAAATAGTATTTGTTGGAAGTAGGTTTATATTGGAATTGAATATGGTGTGTTGTAAGAGATAAAATGTAGTAAGG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:92	YS:i:0	YT:Z:CP
Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1H11_R1_001.fastp-trim.fq.gz_C_to_T.fastq and 1H11_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:
LH00526:197:22KFKVLT4:3:1101:50379:1056_1:N:0:GATAGCCA+CTGTGTTG/1	77	*	0	0	*	*	0	0	ATTTGTTGGAAGTAGGTTTATATTGGAATTGAATATGGTGTGTTGTAAGAGATAAAATGTAGTAAGGTAATAATATAAAAAATTTAATATTA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UP
LH00526:197:22KFKVLT4:3:1101:50379:1056_2:N:0:GATAGCCA+CTGTGTTG/2	141	*	0	0	*	*	0	0	CCTTACTACATTTTATCTCTTACAACACACCATATTCAATTCCAATATAAACCTACTTCCAACAAATACTATTTCTTCTTTCACAAATTATT	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UP

>>> Writing bisulfite mapping results to 1H11_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/1H11_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/1H11_R2_001.fastp-trim.fq.gz
Processed 1000000 sequence pairs so far
Processed 2000000 sequence pairs so far
Processed 3000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00526:197:22KFKVLT4:3:1227:35934:15498_1:N:0:GATAGCCA+CTGTGTTG	ptg000066l	66366
Processed 4000000 sequence pairs so far
Processed 5000000 sequence pairs so far
Processed 6000000 sequence pairs so far
Processed 7000000 sequence pairs so far
Processed 8000000 sequence pairs so far
Processed 9000000 sequence pairs so far
Processed 10000000 sequence pairs so far
Processed 11000000 sequence pairs so far
Processed 12000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00526:197:22KFKVLT4:3:2163:33798:17347_1:N:0:GATAGCCA+CTGTGTTG	ptg000066l	1
Chromosomal sequence could not be extracted for	LH00526:197:22KFKVLT4:3:2163:33806:17361_1:N:0:GATAGCCA+CTGTGTTG	ptg000066l	1
Chromosomal sequence could not be extracted for	LH00526:197:22KFKVLT4:3:2163:33798:17375_1:N:0:GATAGCCA+CTGTGTTG	ptg000066l	1
Processed 13000000 sequence pairs so far
Processed 14000000 sequence pairs so far
Processed 15000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00526:197:22KFKVLT4:3:2317:4561:29016_1:N:0:GATAGCCA+CTGTGTTG	ptg000007l	12295855
Processed 16000000 sequence pairs so far
Processed 17000000 sequence pairs so far
Processed 18000000 sequence pairs so far
Processed 19000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00526:197:22KFKVLT4:4:1116:27721:4278_1:N:0:GATAGCCA+CTGTGTTG	ptg000099l	50605
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
Chromosomal sequence could not be extracted for	LH00526:197:22KFKVLT4:4:1310:32066:7794_1:N:0:GATAGCCA+CTGTGTTG	ptg000066l	1
Processed 25000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00526:197:22KFKVLT4:4:1349:17354:14237_1:N:0:GATAGCCA+CTGTGTTG	ptg000066l	66344
Processed 26000000 sequence pairs so far
Processed 27000000 sequence pairs so far
Processed 28000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00526:197:22KFKVLT4:4:1453:30925:20835_1:N:0:GATAGCCA+CTGTGTTG	ptg000066l	66347
Processed 29000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00526:197:22KFKVLT4:4:1482:31621:19042_1:N:0:GATAGCCA+CTGTGTTG	ptg000066l	66346
Processed 30000000 sequence pairs so far
Processed 31000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00526:197:22KFKVLT4:4:2201:50816:2933_1:N:0:GATAGCCA+CTGTGTTG	ptg000015l	14997092
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
Chromosomal sequence could not be extracted for	LH00526:197:22KFKVLT4:4:2411:11949:12977_1:N:0:GATAGCCA+CTGTGTTG	ptg000066l	66348
Chromosomal sequence could not be extracted for	LH00526:197:22KFKVLT4:4:2444:45847:17977_1:N:0:GATAGCCA+CTGTGTTG	ptg000033l	2625625
Processed 37000000 sequence pairs so far
37970452 reads; of these:
  37970452 (100.00%) were paired; of these:
    15808533 (41.63%) aligned concordantly 0 times
    6676330 (17.58%) aligned concordantly exactly 1 time
    15485589 (40.78%) aligned concordantly >1 times
58.37% overall alignment rate
37970452 reads; of these:
  37970452 (100.00%) were paired; of these:
    15813497 (41.65%) aligned concordantly 0 times
    6676017 (17.58%) aligned concordantly exactly 1 time
    15480938 (40.77%) aligned concordantly >1 times
58.35% overall alignment rate
Processed 37970452 sequences in total

Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, <IN2> line 151881808.
Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, <IN2> line 151881808.
Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, <IN2> line 151881808.
Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, <IN2> line 151881808.

Successfully deleted the temporary files 1H11_R1_001.fastp-trim.fq.gz_C_to_T.fastq and 1H11_R2_001.fastp-trim.fq.gz_G_to_A.fastq

Final Alignment report
======================
Sequence pairs analysed in total:	37970452
Final Cytosine Methylation Report
=================================
Total number of C's analysed:	992770292

Total methylated C's in CpG context:	13247629
Total methylated C's in CHG context:	1064459
Total methylated C's in CHH context:	4116616
Total methylated C's in Unknown context:	50647

Total unmethylated C's in CpG context:	150254801
Total unmethylated C's in CHG context:	170957175
Total unmethylated C's in CHH context:	653129612
Total unmethylated C's in Unknown context:	2436810

C methylated in CpG context:	8.1%
C methylated in CHG context:	0.6%
C methylated in CHH context:	0.6%
C methylated in unknown context (CN or CHN):	2.0%


Bismark completed in 0d 2h 21m 38s

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