Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.5.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools found here: '/srlab/programs/samtools-1.20/samtools'
Reference genome folder provided is /mmfs1/gscratch/scrubbed/sr320/github/project-chilean-mussel/data/Mchi/	(absolute path is '/mmfs1/gscratch/scrubbed/sr320/github/project-chilean-mussel/data/Mchi/)'
FastQ format assumed (by default)
Attention: early reports suggested that high values of -p  to have diminishing returns. Please test different values using a small subset of data for your hardware setting.
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 '/gscratch/scrubbed/sr320/github/project-chilean-mussel/output/06-bismark'):
/mmfs1/gscratch/scrubbed/strigg/analyses/20250731_methylseq/raw-reads/LCo_BSr1_R1.fastq
/mmfs1/gscratch/scrubbed/strigg/analyses/20250731_methylseq/raw-reads/LCo_BSr1_R2.fastq
Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported
Output will be written into the directory: /gscratch/scrubbed/sr320/github/project-chilean-mussel/output/06-bismark/
Setting parallelization to single-threaded (default)

Summary of all aligner options:	-q --score-min L,0,-0.8 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500
Current working directory is: /gscratch/scrubbed/sr320/github/project-chilean-mussel/output/06-bismark

Now reading in and storing sequence information of the genome specified in: /mmfs1/gscratch/scrubbed/sr320/github/project-chilean-mussel/data/Mchi/

Single-core mode: setting pid to 1

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

The provided filenames for paired-end alignments are /mmfs1/gscratch/scrubbed/strigg/analyses/20250731_methylseq/raw-reads/LCo_BSr1_R1.fastq and /mmfs1/gscratch/scrubbed/strigg/analyses/20250731_methylseq/raw-reads/LCo_BSr1_R2.fastq
Input files are in FastQ format
Writing a C -> T converted version of the input file LCo_BSr1_R1.fastq to LCo_BSr1_R1.fastq_C_to_T.fastq
Writing a G -> A converted version of the input file LCo_BSr1_R1.fastq to LCo_BSr1_R1.fastq_G_to_A.fastq

Created C -> T as well as G -> A converted versions of the FastQ file LCo_BSr1_R1.fastq (100000000 sequences in total)

Writing a C -> T converted version of the input file LCo_BSr1_R2.fastq to LCo_BSr1_R2.fastq_C_to_T.fastq
Writing a G -> A converted version of the input file LCo_BSr1_R2.fastq to LCo_BSr1_R2.fastq_G_to_A.fastq

Created C -> T as well as G -> A converted versions of the FastQ file LCo_BSr1_R2.fastq (100000000 sequences in total)

Input files are LCo_BSr1_R1.fastq_C_to_T.fastq and LCo_BSr1_R1.fastq_G_to_A.fastq and LCo_BSr1_R2.fastq_C_to_T.fastq and LCo_BSr1_R2.fastq_G_to_A.fastq (FastQ)
Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /mmfs1/gscratch/scrubbed/sr320/github/project-chilean-mussel/data/Mchi/ with the specified options: -q --score-min L,0,-0.8 -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 LCo_BSr1_R1.fastq_C_to_T.fastq and LCo_BSr1_R2.fastq_G_to_A.fastq, with the options: -q --score-min L,0,-0.8 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc))
Found first alignment:
A01057:543:H2JCGDSXF:1:1101:1669:1000_1:N:0:NTCCGAAT+GAGTTACC/1	77	*	0	0	*	*	0	0	NTTGTTTAAAAATATTTGTATATGTATATTGTATATATTTGTATATTTATTAATGTATGTTTGATATATTTTAAAAAAAAATTAAATTTTAATAATTTGGATAGATTATATAAAATTATATGAGTGAAATTTTATTAATATTTAATTTTAA	#FFFFFFFF:F,F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFF,	YT:Z:UP
A01057:543:H2JCGDSXF:1:1101:1669:1000_2:N:0:NTCCGAAT+GAGTTACC/2	141	*	0	0	*	*	0	0	NAAAAAAAAAAAAAATACAAAAATTATTTAACCTACAACTAAAAACTATATTCTACAACCAAACTACTTNTATATTTCCAACAATACAAAAATAAATATAAACTTATCATAAAATCAAAAATATTAAAAAAAACTTATTATTAAAATTAAA	#FF:FFFFFFFFFF,FFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFF:FFFFFFFFFFFFFFFF:FF:FFFFFFFFF:FFFFF:F	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from LCo_BSr1_R1.fastq_G_to_A.fastq and LCo_BSr1_R2.fastq_C_to_T.fastq, with the options: -q --score-min L,0,-0.8 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc))
Found first alignment:
A01057:543:H2JCGDSXF:1:1101:1669:1000_1:N:0:NTCCGAAT+GAGTTACC/1	77	*	0	0	*	*	0	0	NTTATTTAAAAATATTTATATATATATATTATATATATTTATATATTTATTAATATATATTTAATATATTTTAAAAAAAAATTAAATTTTAATAATTTAAATAAATTATATAAAATTATATAAATAAAATTTTATTAATATTTAATTTTAA	#FFFFFFFF:F,F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFF,	YT:Z:UP
A01057:543:H2JCGDSXF:1:1101:1669:1000_2:N:0:NTCCGAAT+GAGTTACC/2	141	*	0	0	*	*	0	0	NGAAGGAGAGGAGAATATAAAAATTATTTAATTTATAATTAAAAATTATATTTTATAATTAAATTATTTNTATATTTTTAATAATATAAAAATAAATATAAATTTATTATAAAATTAAAAATATTAAAAAAAATTTATTATTAAAATTAAA	#FF:FFFFFFFFFF,FFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFF:FFFFFFFFFFFFFFFF:FF:FFFFFFFFF:FFFFF:F	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from LCo_BSr1_R1.fastq_G_to_A.fastq and LCo_BSr1_R2.fastq_C_to_T.fastq, with the options: -q --score-min L,0,-0.8 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw))
Found first alignment:
A01057:543:H2JCGDSXF:1:1101:1669:1000_1:N:0:NTCCGAAT+GAGTTACC/1	77	*	0	0	*	*	0	0	NTTATTTAAAAATATTTATATATATATATTATATATATTTATATATTTATTAATATATATTTAATATATTTTAAAAAAAAATTAAATTTTAATAATTTAAATAAATTATATAAAATTATATAAATAAAATTTTATTAATATTTAATTTTAA	#FFFFFFFF:F,F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFF,	YT:Z:UP
A01057:543:H2JCGDSXF:1:1101:1669:1000_2:N:0:NTCCGAAT+GAGTTACC/2	141	*	0	0	*	*	0	0	NGAAGGAGAGGAGAATATAAAAATTATTTAATTTATAATTAAAAATTATATTTTATAATTAAATTATTTNTATATTTTTAATAATATAAAAATAAATATAAATTTATTATAAAATTAAAAATATTAAAAAAAATTTATTATTAAAATTAAA	#FF:FFFFFFFFFF,FFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFF:FFFFFFFFFFFFFFFF:FF:FFFFFFFFF:FFFFF:F	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from LCo_BSr1_R1.fastq_C_to_T.fastq and LCo_BSr1_R2.fastq_G_to_A.fastq, with the options: -q --score-min L,0,-0.8 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw))
Found first alignment:
A01057:543:H2JCGDSXF:1:1101:1669:1000_1:N:0:NTCCGAAT+GAGTTACC/1	77	*	0	0	*	*	0	0	NTTGTTTAAAAATATTTGTATATGTATATTGTATATATTTGTATATTTATTAATGTATGTTTGATATATTTTAAAAAAAAATTAAATTTTAATAATTTGGATAGATTATATAAAATTATATGAGTGAAATTTTATTAATATTTAATTTTAA	#FFFFFFFF:F,F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFF,	YT:Z:UP
A01057:543:H2JCGDSXF:1:1101:1669:1000_2:N:0:NTCCGAAT+GAGTTACC/2	141	*	0	0	*	*	0	0	NAAAAAAAAAAAAAATACAAAAATTATTTAACCTACAACTAAAAACTATATTCTACAACCAAACTACTTNTATATTTCCAACAATACAAAAATAAATATAAACTTATCATAAAATCAAAAATATTAAAAAAAACTTATTATTAAAATTAAA	#FF:FFFFFFFFFF,FFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFF:FFFFFFFFFFFFFFFF:FF:FFFFFFFFF:FFFFF:F	YT:Z:UP

>>> Writing bisulfite mapping results to LCo_BSr1_pe.bam <<<

No such file or directory at /srlab/programs/Bismark-0.24.2/bismark line 2564, <__ANONIO__> line 18.
(ERR): bowtie2-align exited with value 141
(ERR): bowtie2-align exited with value 141
(ERR): bowtie2-align exited with value 141
(ERR): bowtie2-align exited with value 141