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 '/mmfs1/gscratch/scrubbed/sr320/github/project-chilean-mussel/output/07-bismark'):
/mmfs1/gscratch/scrubbed/strigg/analyses/20250731_methylseq/raw-reads/LCo_BSr1_R1.fastq.gz
/mmfs1/gscratch/scrubbed/strigg/analyses/20250731_methylseq/raw-reads/LCo_BSr1_R2.fastq.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: /mmfs1/gscratch/scrubbed/sr320/github/project-chilean-mussel/output/07-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: /mmfs1/gscratch/scrubbed/sr320/github/project-chilean-mussel/output/07-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.gz and /mmfs1/gscratch/scrubbed/strigg/analyses/20250731_methylseq/raw-reads/LCo_BSr1_R2.fastq.gz
Input files are in FastQ format
Writing a C -> T converted version of the input file LCo_BSr1_R1.fastq.gz to LCo_BSr1_R1.fastq.gz_C_to_T.fastq

Created C -> T converted version of the FastQ file LCo_BSr1_R1.fastq.gz (100000000 sequences in total)

Writing a G -> A converted version of the input file LCo_BSr1_R2.fastq.gz to LCo_BSr1_R2.fastq.gz_G_to_A.fastq

Created G -> A converted version of the FastQ file LCo_BSr1_R2.fastq.gz (100000000 sequences in total)

Input files are LCo_BSr1_R1.fastq.gz_C_to_T.fastq and LCo_BSr1_R2.fastq.gz_G_to_A.fastq (FastQ)
Now running 2 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.gz_C_to_T.fastq and LCo_BSr1_R2.fastq.gz_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 CTread1GAread2GAgenome (reading in sequences from LCo_BSr1_R1.fastq.gz_C_to_T.fastq and LCo_BSr1_R2.fastq.gz_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 <<<


Reading in the sequence files /mmfs1/gscratch/scrubbed/strigg/analyses/20250731_methylseq/raw-reads/LCo_BSr1_R1.fastq.gz and /mmfs1/gscratch/scrubbed/strigg/analyses/20250731_methylseq/raw-reads/LCo_BSr1_R2.fastq.gz
Processed 1000000 sequence pairs so far
Processed 2000000 sequence pairs so far
Processed 3000000 sequence pairs so far
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
Processed 13000000 sequence pairs so far
Processed 14000000 sequence pairs so far
Processed 15000000 sequence pairs so far
Processed 16000000 sequence pairs so far
Processed 17000000 sequence pairs so far