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/44B_1.fastq.gz
/mmfs1/gscratch/coenv/sr320/cod-bs/44B_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/44B_1.fastq.gz and /mmfs1/gscratch/coenv/sr320/cod-bs/44B_2.fastq.gz
Input files are in FastQ format
Writing a C -> T converted version of the input file 44B_1.fastq.gz to 44B_1.fastq.gz_C_to_T.fastq

Created C -> T converted version of the FastQ file 44B_1.fastq.gz (55918336 sequences in total)

Writing a G -> A converted version of the input file 44B_2.fastq.gz to 44B_2.fastq.gz_G_to_A.fastq

Created G -> A converted version of the FastQ file 44B_2.fastq.gz (55918336 sequences in total)

Input files are 44B_1.fastq.gz_C_to_T.fastq and 44B_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 44B_1.fastq.gz_C_to_T.fastq and 44B_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:
LH00160:538:22WG5VLT4:6:1101:22453:1042_1:N:0:GACGATCT+TCNTGCAT/1	77	*	0	0	*	*	0	0	ANGGAGTTTTTTTTTAAAGTTAATATTGTTGATGAAATTATTATGATGTTTGGGTTAAATTAATTATTAGTTAGATATGTTTGTTTTTTAAGTATTAATTTAAATGTGAATTTTATTTTGTATTTAAGTAGATTATTTATTGTTTTTTTTT	I#9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UP
LH00160:538:22WG5VLT4:6:1101:22453:1042_2:N:0:GACGATCT+TCNTGCAT/2	141	*	0	0	*	*	0	0	AAAAAAAAACAATAAATAATCTACTTAACTACAAAATAAAATTCACATTTAAATTAATACTTAAAAAACAAACATATCTAACTAATAATTAATTTAACCCAAACATCATAATAATTTCATCAACAATATTAACTTTAAAAAAAAACTCCTT	IIIIIIII9II-IIIIIIIIIIIIIII--IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 44B_1.fastq.gz_C_to_T.fastq and 44B_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:
LH00160:538:22WG5VLT4:6:1101:22453:1042_1:N:0:GACGATCT+TCNTGCAT/1	83	NC_082386.1_GA_converted	1127406	40	1M5I145M	=	1127406	-146	AAAAAAAAACAATAAATAATCTACTTAAATACAAAATAAAATTCACATTTAAATTAATACTTAAAAAACAAACATATCTAACTAATAATTAATTTAACCCAAACATCATAATAATTTCATCAACAATATTAACTTTAAAAAAAAACTCCNT	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9#I	AS:i:-27	XN:i:0	XM:i:2	XO:i:1	XG:i:5	NM:i:7	MD:Z:0T143T1	YS:i:-32	YT:Z:CP
LH00160:538:22WG5VLT4:6:1101:22453:1042_2:N:0:GACGATCT+TCNTGCAT/2	163	NC_082386.1_GA_converted	1127406	40	1M5I145M	=	1127406	146	AAAAAAAAACAATAAATAATCTACTTAACTACAAAATAAAATTCACATTTAAATTAATACTTAAAAAACAAACATATCTAACTAATAATTAATTTAACCCAAACATCATAATAATTTCATCAACAATATTAACTTTAAAAAAAAACTCCTT	IIIIIIII9II-IIIIIIIIIIIIIII--IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-32	XN:i:0	XM:i:2	XO:i:1	XG:i:5	NM:i:7	MD:Z:0T22A122	YS:i:-27	YT:Z:CP

>>> Writing bisulfite mapping results to 44B_pe.bam <<<


Reading in the sequence files /mmfs1/gscratch/coenv/sr320/cod-bs/44B_1.fastq.gz and /mmfs1/gscratch/coenv/sr320/cod-bs/44B_2.fastq.gz
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1106:38985:21199_1:N:0:GACGATCT+TCGTGCAT	NC_082390.1	1
Processed 1000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1119:30140:13285_1:N:0:GACGATCT+TCGTGCAT	NC_082385.1	2
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1124:34777:8004_1:N:0:GACGATCT+TCGTGCAT	NC_082399.1	21077819
Processed 2000000 sequence pairs so far
Processed 3000000 sequence pairs so far
Processed 4000000 sequence pairs so far
Processed 5000000 sequence pairs so far
Processed 6000000 sequence pairs so far
Processed 7000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1209:23966:29380_1:N:0:GACGATCT+TCGTGCAT	NC_082396.1	2
Processed 8000000 sequence pairs so far
Processed 9000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1234:50201:17809_1:N:0:GACGATCT+TCGTGCAT	NC_036931.1	1
Processed 10000000 sequence pairs so far
Processed 11000000 sequence pairs so far
Processed 12000000 sequence pairs so far