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/63B_1.fastq.gz
/mmfs1/gscratch/coenv/sr320/cod-bs/63B_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/63B_1.fastq.gz and /mmfs1/gscratch/coenv/sr320/cod-bs/63B_2.fastq.gz
Input files are in FastQ format
Writing a C -> T converted version of the input file 63B_1.fastq.gz to 63B_1.fastq.gz_C_to_T.fastq

Created C -> T converted version of the FastQ file 63B_1.fastq.gz (59843638 sequences in total)

Writing a G -> A converted version of the input file 63B_2.fastq.gz to 63B_2.fastq.gz_G_to_A.fastq

Created G -> A converted version of the FastQ file 63B_2.fastq.gz (59843638 sequences in total)

Input files are 63B_1.fastq.gz_C_to_T.fastq and 63B_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 63B_1.fastq.gz_C_to_T.fastq and 63B_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:
LH00160:538:22WG5VLT4:6:1101:23051:1042_1:N:0:CCTTGATC+GANGGAGT/1	99	NC_082397.1_CT_converted	27110892	1	151M	=	27110953	212	ANATTGTTGATTTTATTTAAAATGAATGTATTTTATTTTTAAATGGTTTAGTATGGTTTAATAATTTTTTAGTAAGTTTAGTAATATGTTTGAATTGAAATTGATATAGATATTAATGTTTTTTGTTTTTATGTTTGTAAAATGTTTTTTA	I#IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-1	XS:i:-1	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:1T149	YS:i:-6	YT:Z:CP
LH00160:538:22WG5VLT4:6:1101:23051:1042_2:N:0:CCTTGATC+GANGGAGT/2	147	NC_082397.1_CT_converted	27110953	1	151M	=	27110892	-212	TAATTTTTTAGTAAGTTTAGTAATATGTTTGAATTGAAATTGATATAGATATTAATGTTTTTTGTTTTTATGTTTGTAAAATGTTTTTTAGAGTGTTAGAATTATTTTTTGATAGATAATGTGTTTTTGATTTTATATGGTTGATTTTTTT	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:148A2	YS:i:-1	YT:Z:CP
Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 63B_1.fastq.gz_C_to_T.fastq and 63B_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:
LH00160:538:22WG5VLT4:6:1101:23051:1042_1:N:0:CCTTGATC+GANGGAGT/1	83	NC_082401.1_GA_converted	3308707	1	151M	=	3308646	-212	TAAAAAACATTTTACAAACATAAAAACAAAAAACATTAATATCTATATCAATTTCAATTCAAACATATTACTAAACTTACTAAAAAATTATTAAACCATACTAAACCATTTAAAAATAAAATACATTCATTTTAAATAAAATCAACAATNT	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII#I	AS:i:-1	XS:i:-1	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:149A1	YS:i:-6	YT:Z:CP
LH00160:538:22WG5VLT4:6:1101:23051:1042_2:N:0:CCTTGATC+GANGGAGT/2	163	NC_082401.1_GA_converted	3308646	1	151M	=	3308707	212	AAAAAAATCAACCATATAAAATCAAAAACACATTATCTATCAAAAAATAATTCTAACACTCTAAAAAACATTTTACAAACATAAAAACAAAAAACATTAATATCTATATCAATTTCAATTCAAACATATTACTAAACTTACTAAAAAATTA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:2T148	YS:i:-1	YT:Z:CP

>>> Writing bisulfite mapping results to 63B_pe.bam <<<


Reading in the sequence files /mmfs1/gscratch/coenv/sr320/cod-bs/63B_1.fastq.gz and /mmfs1/gscratch/coenv/sr320/cod-bs/63B_2.fastq.gz
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1107:43614:27979_1:N:0:CCTTGATC+GATGGAGT	NC_082382.1	26289603
Processed 1000000 sequence pairs so far