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/13B_1.fastq.gz
/mmfs1/gscratch/coenv/sr320/cod-bs/13B_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/13B_1.fastq.gz and /mmfs1/gscratch/coenv/sr320/cod-bs/13B_2.fastq.gz
Input files are in FastQ format
Writing a C -> T converted version of the input file 13B_1.fastq.gz to 13B_1.fastq.gz_C_to_T.fastq

Created C -> T converted version of the FastQ file 13B_1.fastq.gz (67778298 sequences in total)

Writing a G -> A converted version of the input file 13B_2.fastq.gz to 13B_2.fastq.gz_G_to_A.fastq

Created G -> A converted version of the FastQ file 13B_2.fastq.gz (67778298 sequences in total)

Input files are 13B_1.fastq.gz_C_to_T.fastq and 13B_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 13B_1.fastq.gz_C_to_T.fastq and 13B_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:
LH00160:538:22WG5VLT4:6:1101:27518:1042_1:N:0:CGCATGAT+AANCCTGA/1	77	*	0	0	*	*	0	0	GNTGTTTAATTTAATTTTATATTTTTTTATTTAATAGATTTTTGTTGGATTTATATTTATTTTTAATGATATAATAAATGATATTAGTTAAATGTAATTTATTGTTATTAAATTATATGGGGTTATTTTTTTTTTTTTTTTTTTTAATTTG	I#IIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UP
LH00160:538:22WG5VLT4:6:1101:27518:1042_2:N:0:CGCATGAT+AANCCTGA/2	141	*	0	0	*	*	0	0	AAAAATATATTTAAAAACAAAAATTTAAAAAAATACATATAAAACAATTAAAAACTAACCAAATAACAACCATTAAAACAAATCTACACTCCCATCACAACTATAAAAATATTTTATCAAATCATCAAAAAAACATAAATATAATTTACAT	III9IIIIIIIIIIIIIIIIIIIIIII9I9IIIIIIIIIII9IIIIIIIIIIIII-IIIIIIIII-IIIIIIIIIIIIIIII9II9IIIIIII-I9III9IIIII-IIIIIIIIIIIIIIIIIIIII9II-IIIIIIIIIIII-IIIIIII	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 13B_1.fastq.gz_C_to_T.fastq and 13B_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:
LH00160:538:22WG5VLT4:6:1101:27518:1042_1:N:0:CGCATGAT+AANCCTGA/1	77	*	0	0	*	*	0	0	GNTGTTTAATTTAATTTTATATTTTTTTATTTAATAGATTTTTGTTGGATTTATATTTATTTTTAATGATATAATAAATGATATTAGTTAAATGTAATTTATTGTTATTAAATTATATGGGGTTATTTTTTTTTTTTTTTTTTTTAATTTG	I#IIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UP
LH00160:538:22WG5VLT4:6:1101:27518:1042_2:N:0:CGCATGAT+AANCCTGA/2	141	*	0	0	*	*	0	0	AAAAATATATTTAAAAACAAAAATTTAAAAAAATACATATAAAACAATTAAAAACTAACCAAATAACAACCATTAAAACAAATCTACACTCCCATCACAACTATAAAAATATTTTATCAAATCATCAAAAAAACATAAATATAATTTACAT	III9IIIIIIIIIIIIIIIIIIIIIII9I9IIIIIIIIIII9IIIIIIIIIIIII-IIIIIIIII-IIIIIIIIIIIIIIII9II9IIIIIII-I9III9IIIII-IIIIIIIIIIIIIIIIIIIII9II-IIIIIIIIIIII-IIIIIII	YT:Z:UP

>>> Writing bisulfite mapping results to 13B_pe.bam <<<


Reading in the sequence files /mmfs1/gscratch/coenv/sr320/cod-bs/13B_1.fastq.gz and /mmfs1/gscratch/coenv/sr320/cod-bs/13B_2.fastq.gz
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1105:28141:1420_1:N:0:CGCATGAT+AAGCCTGA	NC_082386.1	22175831
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1116:24718:12388_1:N:0:CGCATGAT+AAGCCTGA	NC_082395.1	2
Processed 1000000 sequence pairs so far
Processed 2000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1134:27211:27909_1:N:0:CGCATGAT+AAGCCTGA	NC_082387.1	3
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1143:10444:7514_1:N:0:CGCATGAT+AAGCCTGA	NC_082392.1	2
Processed 3000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1160:49432:19896_1:N:0:CGCATGAT+AAGCCTGA	NC_082400.1	17993468
Processed 4000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1167:13996:20443_1:N:0:CGCATGAT+AAGCCTGA	NC_082386.1	22175834
Processed 5000000 sequence pairs so far
Processed 6000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1192:42416:18314_1:N:0:CGCATGAT+AAGCCTGA	NC_082397.1	1
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1206:31386:8494_1:N:0:CGCATGAT+AAGCCTGA	NC_082400.1	17993475
Processed 7000000 sequence pairs so far