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/23B_1.fastq.gz
/mmfs1/gscratch/coenv/sr320/cod-bs/23B_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/23B_1.fastq.gz and /mmfs1/gscratch/coenv/sr320/cod-bs/23B_2.fastq.gz
Input files are in FastQ format
Writing a C -> T converted version of the input file 23B_1.fastq.gz to 23B_1.fastq.gz_C_to_T.fastq

Created C -> T converted version of the FastQ file 23B_1.fastq.gz (57338827 sequences in total)

Writing a G -> A converted version of the input file 23B_2.fastq.gz to 23B_2.fastq.gz_G_to_A.fastq

Created G -> A converted version of the FastQ file 23B_2.fastq.gz (57338827 sequences in total)

Input files are 23B_1.fastq.gz_C_to_T.fastq and 23B_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 23B_1.fastq.gz_C_to_T.fastq and 23B_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:
LH00160:538:22WG5VLT4:6:1101:21918:1042_1:N:0:GCAAGATC+AGNCGAAG/1	99	NC_082386.1_CT_converted	3511178	1	151M	=	3511286	259	ANTGTAATTTTTAATGTTTTATGTGATGTAATTTGGTTTTATATTTTGTTTTTGTGTTGTTTGTAGTTTGGTTTGGGTTTGTTTTATTTGATTTTTTGGGGAGTGTAGAGAAGTAAAGGGTGATAGGGAATAGTTTTAATTATTTTTTTAA	I#IIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIII	AS:i:-19	XS:i:-19	XN:i:0	XM:i:4	XO:i:0	XG:i:0	NM:i:4	MD:Z:1A11G46A64A25	YS:i:-60	YT:Z:CP
LH00160:538:22WG5VLT4:6:1101:21918:1042_2:N:0:GCAAGATC+AGNCGAAG/2	147	NC_082386.1_CT_converted	3511286	1	151M	=	3511178	-259	AGAAGTAAAGGGTGATAGGGAATAGTTTTAATTATTTTTTTAATTTTTGAAGAAATTTTAATTAATAGATTAATATTTGGTTAATAAATGTTTTTGGTTTATTGGGGGTTAATTGTTTTTAAGGATTTGATTTAAGTTTTTTTTTTTTTTT	IIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIII	AS:i:-60	XS:i:-54	XN:i:0	XM:i:10	XO:i:0	XG:i:0	NM:i:10	MD:Z:17A70G16A31G1A1A0A0A0A0G5	YS:i:-19	YT:Z:CP
Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 23B_1.fastq.gz_C_to_T.fastq and 23B_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:
LH00160:538:22WG5VLT4:6:1101:21918:1042_1:N:0:GCAAGATC+AGNCGAAG/1	83	NC_082391.1_GA_converted	10317427	11	151M	=	10317319	-259	TTAAAAAAATAATTAAAACTATTCCCTATCACCCTTTACTTCTCTACACTCCCCAAAAAATCAAATAAAACAAACCCAAACCAAACTACAAACAACACAAAAACAAAATATAAAACCAAATTACATCACATAAAACATTAAAAATTACANT	IIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIII#I	AS:i:-7	XS:i:-54	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:25T123T1	YS:i:-48	YT:Z:CP
LH00160:538:22WG5VLT4:6:1101:21918:1042_2:N:0:GCAAGATC+AGNCGAAG/2	163	NC_082391.1_GA_converted	10317319	11	151M	=	10317427	259	AAAAAAAAAAAAAAACTTAAATCAAATCCTTAAAAACAATTAACCCCCAATAAACCAAAAACATTTATTAACCAAATATTAATCTATTAATTAAAATTTCTTCAAAAATTAAAAAAATAATTAAAACTATTCCCTATCACCCTTTACTTCT	IIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIII	AS:i:-48	XS:i:-70	XN:i:0	XM:i:8	XO:i:0	XG:i:0	NM:i:8	MD:Z:5C0T0T0T0T1T1C119T17	YS:i:-7	YT:Z:CP

>>> Writing bisulfite mapping results to 23B_pe.bam <<<


Reading in the sequence files /mmfs1/gscratch/coenv/sr320/cod-bs/23B_1.fastq.gz and /mmfs1/gscratch/coenv/sr320/cod-bs/23B_2.fastq.gz
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1109:9537:6365_1:N:0:GCAAGATC+AGTCGAAG	NC_082394.1	22312305
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1109:16917:12893_1:N:0:GCAAGATC+AGTCGAAG	NC_082386.1	22175842
Processed 1000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1118:5742:3045_1:N:0:GCAAGATC+AGTCGAAG	NC_082398.1	1
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1118:37399:6967_1:N:0:GCAAGATC+AGTCGAAG	NC_036931.1	16434
Processed 2000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1131:33571:7261_1:N:0:GCAAGATC+AGTCGAAG	NC_082399.1	21077815
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1134:35238:2191_1:N:0:GCAAGATC+AGTCGAAG	NC_082386.1	22175840
Processed 3000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1143:22898:15176_1:N:0:GCAAGATC+AGTCGAAG	NC_082394.1	22312321
Processed 4000000 sequence pairs so far