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_BSr3_R1.fastq.gz
/mmfs1/gscratch/scrubbed/strigg/analyses/20250731_methylseq/raw-reads/LCo_BSr3_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_BSr3_R1.fastq.gz and /mmfs1/gscratch/scrubbed/strigg/analyses/20250731_methylseq/raw-reads/LCo_BSr3_R2.fastq.gz
Input files are in FastQ format
Writing a C -> T converted version of the input file LCo_BSr3_R1.fastq.gz to LCo_BSr3_R1.fastq.gz_C_to_T.fastq

Created C -> T converted version of the FastQ file LCo_BSr3_R1.fastq.gz (100000000 sequences in total)

Writing a G -> A converted version of the input file LCo_BSr3_R2.fastq.gz to LCo_BSr3_R2.fastq.gz_G_to_A.fastq

Created G -> A converted version of the FastQ file LCo_BSr3_R2.fastq.gz (100000000 sequences in total)

Input files are LCo_BSr3_R1.fastq.gz_C_to_T.fastq and LCo_BSr3_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_BSr3_R1.fastq.gz_C_to_T.fastq and LCo_BSr3_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:1:1101:1506:1000_1:N:0:NTCACTCG+GTGCTATG/1	99	Chromosome_9_CT_converted	5083615	6	151M	=	5083717	257	NTTAAGTATATAGAATATAAAAATGGTTGATAATGTGATGGATTGATAGATGGTAAAATAGTATAAAAAATATTTATTAAGTTTTGTTAATTTGTAGTGATTTGTAATATATGGTAAAAATATAATTATATGGTATTTTGTTATTTTGTAG	#FFFFF:F::FFFFFF,FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFF:F:FFFFFFFF:FFFFFFFFFFF,FF:FF:FF:FF::FFFF::FFFFFFFF	AS:i:-7	XS:i:-13	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:0A138A11	YS:i:-43	YT:Z:CP
A01057:543:H2JCGDSXF:1:1101:1506:1000_2:N:0:NTCACTCG+GTGCTATG/2	147	Chromosome_9_CT_converted	5083717	6	119M4D32M	=	5083615	-257	TGTAATATATGGTAAAAATATAATTATATGGTATTTTGTTATTTTGTAGTGATTTGTAGTATTATATATAAATATATATGTNTGTGTGTGTTATTAATTTATTAGTATTTAGAGGATTATATTTGTATTGGATTAATATTTTTTTTTTTTN	FFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF,FFFFFFFFFF:FF:FFFFFFFFFFFFFF#	AS:i:-43	XS:i:-49	XN:i:0	XM:i:6	XO:i:1	XG:i:4	NM:i:10	MD:Z:37A20A4G17T37^TATT24A6T0	YS:i:-7	YT:Z:CP
Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from LCo_BSr3_R1.fastq.gz_C_to_T.fastq and LCo_BSr3_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:1:1101:1506:1000_1:N:0:NTCACTCG+GTGCTATG/1	77	*	0	0	*	*	0	0	NTTAAGTATATAGAATATAAAAATGGTTGATAATGTGATGGATTGATAGATGGTAAAATAGTATAAAAAATATTTATTAAGTTTTGTTAATTTGTAGTGATTTGTAATATATGGTAAAAATATAATTATATGGTATTTTGTTATTTTGTAG	#FFFFF:F::FFFFFF,FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFF:F:FFFFFFFF:FFFFFFFFFFF,FF:FF:FF:FF::FFFF::FFFFFFFF	YT:Z:UP
A01057:543:H2JCGDSXF:1:1101:1506:1000_2:N:0:NTCACTCG+GTGCTATG/2	141	*	0	0	*	*	0	0	NAAAAAAAAAAAATATTAATCCAATACAAATATAATCCTCTAAATACTAATAAATTAATAACACACACANACATATATATTTATATATAATACTACAAATCACTACAAAATAACAAAATACCATATAATTATATTTTTACCATATATTACA	#FFFFFFFFFFFFFF:FF:FFFFFFFFFF,FFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFF	YT:Z:UP

>>> Writing bisulfite mapping results to LCo_BSr3_pe.bam <<<


Reading in the sequence files /mmfs1/gscratch/scrubbed/strigg/analyses/20250731_methylseq/raw-reads/LCo_BSr3_R1.fastq.gz and /mmfs1/gscratch/scrubbed/strigg/analyses/20250731_methylseq/raw-reads/LCo_BSr3_R2.fastq.gz
Chromosomal sequence could not be extracted for	A01057:543:H2JCGDSXF:1:1109:4734:15859_1:N:0:CTCACTCG+GTGCTATG	Chromosome_12	2
Processed 1000000 sequence pairs so far
Chromosomal sequence could not be extracted for	A01057:543:H2JCGDSXF:1:1116:13910:23171_1:N:0:CTCACTCA+GTGCTATG	Chromosome_12	123051339
Processed 2000000 sequence pairs so far
Processed 3000000 sequence pairs so far
Processed 4000000 sequence pairs so far