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/24B_1.fastq.gz
/mmfs1/gscratch/coenv/sr320/cod-bs/24B_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/24B_1.fastq.gz and /mmfs1/gscratch/coenv/sr320/cod-bs/24B_2.fastq.gz
Input files are in FastQ format
Writing a C -> T converted version of the input file 24B_1.fastq.gz to 24B_1.fastq.gz_C_to_T.fastq

Created C -> T converted version of the FastQ file 24B_1.fastq.gz (64499170 sequences in total)

Writing a G -> A converted version of the input file 24B_2.fastq.gz to 24B_2.fastq.gz_G_to_A.fastq

Created G -> A converted version of the FastQ file 24B_2.fastq.gz (64499170 sequences in total)

Input files are 24B_1.fastq.gz_C_to_T.fastq and 24B_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 24B_1.fastq.gz_C_to_T.fastq and 24B_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:
LH00160:538:22WG5VLT4:6:1101:23812:1042_1:N:0:GCTATCCT+AANAGGTG/1	99	NC_082388.1_CT_converted	8694974	4	133M8I10M	=	8694966	-151	ANTAGTATTTTGTTAATGAGGGAATTGAAGTTATTTTTGTTTATGGTTGTTGGGTTATAGTTGGTTTTTTGTGGTTTTATTTTTTTTTTTTGATTGGTTTTGGTTAGATGTTTTTTGAGGGTTGGATGTAGTGGATTTTTAGATTGGAAGA	I#IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-48	XS:i:-106	XN:i:0	XM:i:4	XO:i:1	XG:i:8	NM:i:12	MD:Z:1T136T2T0G0	YS:i:-38	YT:Z:CP
LH00160:538:22WG5VLT4:6:1101:23812:1042_2:N:0:GCTATCCT+AANAGGTG/2	147	NC_082388.1_CT_converted	8694966	4	5M3I143M	=	8694974	151	TTTTTTGATTTATTAGTATTTTGTTAATGAGGGAATTGAAGTTATTTTTGGTTATGGTTGTTGGGTTATAGTTGGTTTTTTGTGGTTTTATTTTTTTTTTTTGATTGGTTTTGGTTAGATGTTTTTTGAGGGTTGGATGTAGTGGATTTTT	IIIIIIII9I9I9IIIIII9IIII9IIIIIIIIIIIIIIIIIII9III9I-II9I9IIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-38	XS:i:-97	XN:i:0	XM:i:4	XO:i:1	XG:i:3	NM:i:7	MD:Z:1A45T97G1A0	YS:i:-48	YT:Z:CP
Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 24B_1.fastq.gz_C_to_T.fastq and 24B_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:
LH00160:538:22WG5VLT4:6:1101:23812:1042_1:N:0:GCTATCCT+AANAGGTG/1	77	*	0	0	*	*	0	0	ANTAGTATTTTGTTAATGAGGGAATTGAAGTTATTTTTGTTTATGGTTGTTGGGTTATAGTTGGTTTTTTGTGGTTTTATTTTTTTTTTTTGATTGGTTTTGGTTAGATGTTTTTTGAGGGTTGGATGTAGTGGATTTTTAGATTGGAAGA	I#IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UP
LH00160:538:22WG5VLT4:6:1101:23812:1042_2:N:0:GCTATCCT+AANAGGTG/2	141	*	0	0	*	*	0	0	AAAAATCCACTACATCCAACCCTCAAAAAACATCTAACCAAAACCAATCAAAAAAAAAAAATAAAACCACAAAAAACCAACTATAACCCAACAACCATAACCAAAAATAACTTCAATTCCCTCATTAACAAAATACTAATAAATCAAAAAA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIII9I9II-I9III9IIIIIIIIIIIIIIIIIII9IIII9IIIIII9I9I9IIIIIIII	YT:Z:UP

>>> Writing bisulfite mapping results to 24B_pe.bam <<<


Reading in the sequence files /mmfs1/gscratch/coenv/sr320/cod-bs/24B_1.fastq.gz and /mmfs1/gscratch/coenv/sr320/cod-bs/24B_2.fastq.gz
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1107:33782:18832_1:N:0:GCTATCCT+AACAGGTG	NC_082399.1	21077814
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1112:25787:13313_1:N:0:GCTATCCT+AACAGGTG	NC_082386.1	22175832
Processed 1000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1114:3549:2359_1:N:0:GCTATCCT+AACAGGTG	NC_036931.1	16454
Processed 2000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1130:34389:22348_1:N:0:GCTATCCT+AACAGGTG	NC_082390.1	23393727
Processed 3000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1139:7085:10805_1:N:0:GCTATCCT+AACAGGTG	NC_082398.1	1
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1145:11730:20583_1:N:0:GCTATCCT+AACAGGTG	NC_036931.1	1
Processed 4000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1154:30553:16577_1:N:0:GCTATCCT+AACAGGTG	NC_082399.1	21077818
Processed 5000000 sequence pairs so far