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/31B_1.fastq.gz
/mmfs1/gscratch/coenv/sr320/cod-bs/31B_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/31B_1.fastq.gz and /mmfs1/gscratch/coenv/sr320/cod-bs/31B_2.fastq.gz
Input files are in FastQ format
Writing a C -> T converted version of the input file 31B_1.fastq.gz to 31B_1.fastq.gz_C_to_T.fastq

Created C -> T converted version of the FastQ file 31B_1.fastq.gz (66926704 sequences in total)

Writing a G -> A converted version of the input file 31B_2.fastq.gz to 31B_2.fastq.gz_G_to_A.fastq

Created G -> A converted version of the FastQ file 31B_2.fastq.gz (66926704 sequences in total)

Input files are 31B_1.fastq.gz_C_to_T.fastq and 31B_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 31B_1.fastq.gz_C_to_T.fastq and 31B_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:
LH00160:538:22WG5VLT4:6:1101:24686:1042_1:N:0:TACGCTAC+CGNGTGAT/1	99	NC_082383.1_CT_converted	21504544	7	151M	=	21504651	251	TNTAAAAATTATAAAATGATTATTAATGTAGGTTATGTGGAAAATGTGTTGATTTTGGTTTAGTTTGGTTTTGTTTTTTTTGTTATGTAGTTGGTTGGTTAAAATGGTTGTTGTTGAGTATGGGGAGTGTTTTTTAATTTATATTTTAGGA	I#II9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-7	XS:i:-53	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:1A133G15	YS:i:-50	YT:Z:CP
LH00160:538:22WG5VLT4:6:1101:24686:1042_2:N:0:TACGCTAC+CGNGTGAT/2	147	NC_082383.1_CT_converted	21504651	7	140M7I4M	=	21504544	-251	TTGTTGTTGAGTATGGGGAGTGTTTTTTAATTTATATTTTAGGATTTGTTTGTTTTGAGTATGGTATTTGGGTTTTAGAAGTATATTTTTTTTTGTTGGATTTTATTTAAATTTTGGTTAGTAAGTATGGATAGTATGGGTTTTTTTTTTT	IIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-50	XS:i:-50	XN:i:0	XM:i:4	XO:i:1	XG:i:7	NM:i:11	MD:Z:28G17A29T64A2	YS:i:-7	YT:Z:CP
Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 31B_1.fastq.gz_C_to_T.fastq and 31B_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:
LH00160:538:22WG5VLT4:6:1101:24686:1042_1:N:0:TACGCTAC+CGNGTGAT/1	83	NC_082395.1_GA_converted	21147533	0	51M8I71M2D21M	=	21147433	-245	TCCTAAAATATAAATTAAAAAACACTCCCCATACTCAACAACAACCATTTTAACCAACCAACTACATAACAAAAAAAACAAAACCAAACTAAACCAAAATCAACACATTTTCCACATAACCTACATTAATAATCATTTTATAATTTTTANA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II#I	AS:i:-53	XS:i:-53	XN:i:0	XM:i:3	XO:i:2	XG:i:10	NM:i:13	MD:Z:15C32C73^AA19T1	YS:i:-50	YT:Z:CP
LH00160:538:22WG5VLT4:6:1101:24686:1042_2:N:0:TACGCTAC+CGNGTGAT/2	163	NC_082395.1_GA_converted	21147433	0	3M7I141M	=	21147533	245	AAAAAAAAAAACCCATACTATCCATACTTACTAACCAAAATTTAAATAAAATCCAACAAAAAAAAATATACTTCTAAAACCCAAATACCATACTCAAAACAAACAAATCCTAAAATATAAATTAAAAAACACTCCCCATACTCAACAACAA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIII	AS:i:-50	XS:i:-50	XN:i:0	XM:i:4	XO:i:1	XG:i:7	NM:i:11	MD:Z:2T64A29T17C28	YS:i:-53	YT:Z:CP

>>> Writing bisulfite mapping results to 31B_pe.bam <<<


Reading in the sequence files /mmfs1/gscratch/coenv/sr320/cod-bs/31B_1.fastq.gz and /mmfs1/gscratch/coenv/sr320/cod-bs/31B_2.fastq.gz
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1101:12920:18916_1:N:0:TACGCTAC+CGTGTGAT	NC_082399.1	21077817
Processed 1000000 sequence pairs so far
Processed 2000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1126:18730:27377_1:N:0:TACGCTAC+CGTGTGAT	NC_082399.1	21077819
Processed 3000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1139:21668:20135_1:N:0:TACGCTAC+CGTGTGAT	NC_082399.1	21077820
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1139:21676:20149_1:N:0:TACGCTAC+CGTGTGAT	NC_082399.1	21077820
Processed 4000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1149:41388:15386_1:N:0:TACGCTAA+CGTGTGAT	NC_036931.1	2
Processed 5000000 sequence pairs so far
Processed 6000000 sequence pairs so far
Processed 7000000 sequence pairs so far