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-cod-temperature/data/genome/	(absolute path is '/mmfs1/gscratch/scrubbed/sr320/github/project-cod-temperature/data/genome/)'
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-cod-temperature/output/16-bismark'):
/mmfs1/gscratch/coenv/sr320/cod-bs/22B_1.fastq.gz
/mmfs1/gscratch/coenv/sr320/cod-bs/22B_2.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-cod-temperature/output/16-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-cod-temperature/output/16-bismark

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

Single-core mode: setting pid to 1

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

The provided filenames for paired-end alignments are /mmfs1/gscratch/coenv/sr320/cod-bs/22B_1.fastq.gz and /mmfs1/gscratch/coenv/sr320/cod-bs/22B_2.fastq.gz
Input files are in FastQ format
Writing a C -> T converted version of the input file 22B_1.fastq.gz to 22B_1.fastq.gz_C_to_T.fastq

Created C -> T converted version of the FastQ file 22B_1.fastq.gz (50513557 sequences in total)

Writing a G -> A converted version of the input file 22B_2.fastq.gz to 22B_2.fastq.gz_G_to_A.fastq

Created G -> A converted version of the FastQ file 22B_2.fastq.gz (50513557 sequences in total)

Input files are 22B_1.fastq.gz_C_to_T.fastq and 22B_2.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-cod-temperature/data/genome/ 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 22B_1.fastq.gz_C_to_T.fastq and 22B_2.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:
LH00160:538:22WG5VLT4:6:1101:22242:1042_1:N:0:ATCGATCG+TGNAAGCA/1	77	*	0	0	*	*	0	0	ANATAGTATTATTAGAGTAAGTTTATAATTTAATTTAGTTTATATTTAAATTATTAGTATGGAGGTTGGTAATATAGTATTAAAGTAAATTAATAGTAAAAATTAAATTATATATTTAATATTTGAAATGAGGTTAATTTAATTTTAGATT	I#III-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UP
LH00160:538:22WG5VLT4:6:1101:22242:1042_2:N:0:ATCGATCG+TGNAAGCA/2	141	*	0	0	*	*	0	0	AAAAAAAAAATAACACTAACATACAAACCTCAAATATTTAAAAATCTAAAATTAAATTAACCTCATTTCAAATATTAAATATATAATTTAATTTTTACTATTAATTTACTTTAATACTATATTACCAACCTCCATACTAATAATTTAAATA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIII9IIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 22B_1.fastq.gz_C_to_T.fastq and 22B_2.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:
LH00160:538:22WG5VLT4:6:1101:22242:1042_1:N:0:ATCGATCG+TGNAAGCA/1	83	NC_082403.1_GA_converted	4205354	42	151M	=	4205318	-187	AATCTAAAATTAAATTAACCTCATTTCAAATATTAAATATATAATTTAATTTTTACTATTAATTTACTTTAATACTATATTACCAACCTCCATACTAATAATTTAAATATAAACTAAATTAAATTATAAACTTACTCTAATAATACTATNT	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-III#I	AS:i:-1	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:149A1	YS:i:-35	YT:Z:CP
LH00160:538:22WG5VLT4:6:1101:22242:1042_2:N:0:ATCGATCG+TGNAAGCA/2	163	NC_082403.1_GA_converted	4205318	42	4M6I141M	=	4205354	187	AAAAAAAAAATAACACTAACATACAAACCTCAAATATTTAAAAATCTAAAATTAAATTAACCTCATTTCAAATATTAAATATATAATTTAATTTTTACTATTAATTTACTTTAATACTATATTACCAACCTCCATACTAATAATTTAAATA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIII9IIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-35	XN:i:0	XM:i:2	XO:i:1	XG:i:6	NM:i:8	MD:Z:0C2T141	YS:i:-1	YT:Z:CP

>>> Writing bisulfite mapping results to 22B_pe.bam <<<


Reading in the sequence files /mmfs1/gscratch/coenv/sr320/cod-bs/22B_1.fastq.gz and /mmfs1/gscratch/coenv/sr320/cod-bs/22B_2.fastq.gz
Processed 1000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1130:40773:10343_1:N:0:ATCGATCG+TGGAAGCA	NC_082398.1	3
Processed 2000000 sequence pairs so far
Processed 3000000 sequence pairs so far
Processed 4000000 sequence pairs so far
Processed 5000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1205:42376:12500_1:N:0:ATCGATCG+TGGAAGCA	NC_082396.1	1
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1218:20438:10749_1:N:0:ATCGATCG+TGGAAGCA	NC_082399.1	21077815
Processed 6000000 sequence pairs so far
Processed 7000000 sequence pairs so far