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/09B_1.fastq.gz
/mmfs1/gscratch/coenv/sr320/cod-bs/09B_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/09B_1.fastq.gz and /mmfs1/gscratch/coenv/sr320/cod-bs/09B_2.fastq.gz
Input files are in FastQ format
Writing a C -> T converted version of the input file 09B_1.fastq.gz to 09B_1.fastq.gz_C_to_T.fastq

Created C -> T converted version of the FastQ file 09B_1.fastq.gz (50872910 sequences in total)

Writing a G -> A converted version of the input file 09B_2.fastq.gz to 09B_2.fastq.gz_G_to_A.fastq

Created G -> A converted version of the FastQ file 09B_2.fastq.gz (50872910 sequences in total)

Input files are 09B_1.fastq.gz_C_to_T.fastq and 09B_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 09B_1.fastq.gz_C_to_T.fastq and 09B_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:
LH00160:538:22WG5VLT4:6:1101:22598:1042_1:N:0:TTCCAAGG+CTNCAAGG/1	99	NC_082388.1_CT_converted	6902071	42	151M	=	6902081	154	TNTGGTTTTAGTATTTTAGTAATTTTGGATTGTTTAGTTTTAGGTGTATGTGTATAGTAGTAGTTAGTTAGTGAGAGTAGTAGTAGAGAAGTGATTGTTGTTGTTTGTGTATTTTTGGAGTATTATAGTATATTTATATAATATTATATTT	I#9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII9IIIIIIIIIIIIIIIIIII	AS:i:-7	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:1T148A0	YS:i:-38	YT:Z:CP
LH00160:538:22WG5VLT4:6:1101:22598:1042_2:N:0:TTCCAAGG+CTNCAAGG/2	147	NC_082388.1_CT_converted	6902081	42	138M7I6M	=	6902071	-154	GTATTTTAGTAATTTTGGATTGTTTAGTTTTAGGTGTATGTGTATAGTAGTAGTTAGTTAGTGAGAGTAGTAGTAGAGAAGTGATTGTTGTTGTTTGTGTATTTTTGGAGTATTATAGTATATTTATATAATATTATATTTTTTTTTTTTT	IIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-38	XN:i:0	XM:i:2	XO:i:1	XG:i:7	NM:i:9	MD:Z:140A1A1	YS:i:-7	YT:Z:CP
Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 09B_1.fastq.gz_C_to_T.fastq and 09B_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:
LH00160:538:22WG5VLT4:6:1101:22598:1042_1:N:0:TTCCAAGG+CTNCAAGG/1	77	*	0	0	*	*	0	0	TNTGGTTTTAGTATTTTAGTAATTTTGGATTGTTTAGTTTTAGGTGTATGTGTATAGTAGTAGTTAGTTAGTGAGAGTAGTAGTAGAGAAGTGATTGTTGTTGTTTGTGTATTTTTGGAGTATTATAGTATATTTATATAATATTATATTT	I#9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII9IIIIIIIIIIIIIIIIIII	YT:Z:UP
LH00160:538:22WG5VLT4:6:1101:22598:1042_2:N:0:TTCCAAGG+CTNCAAGG/2	141	*	0	0	*	*	0	0	AAAAAAAAAAAAATATAATATTATATAAATATACTATAATACTCCAAAAATACACAAACAACAACAATCACTTCTCTACTACTACTCTCACTAACTAACTACTACTATACACATACACCTAAAACTAAACAATCCAAAATTACTAAAATAC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIII	YT:Z:UP

>>> Writing bisulfite mapping results to 09B_pe.bam <<<


Reading in the sequence files /mmfs1/gscratch/coenv/sr320/cod-bs/09B_1.fastq.gz and /mmfs1/gscratch/coenv/sr320/cod-bs/09B_2.fastq.gz
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1109:38491:18664_1:N:0:TTCCAAGG+CTACAAGG	NC_082395.1	2
Processed 1000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1117:5078:9433_1:N:0:TTCCAAGG+CTACAAGG	NC_082399.1	21077815
Processed 2000000 sequence pairs so far
Processed 3000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1148:1089:28749_1:N:0:TTCCAAGG+NTACAAGG	NC_036931.1	1
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1155:40490:25682_1:N:0:TTCCAAGG+CTACAAGG	NC_082392.1	2
Processed 4000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1167:27818:9853_1:N:0:TTCCAAGG+CTACAAGG	NC_082393.1	1
Processed 5000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1180:40846:16044_1:N:0:TTCCAAGG+CTACAAGG	NC_082383.1	1
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1180:40838:16058_1:N:0:TTCCAAGG+CTACAAGG	NC_082383.1	1
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1180:40822:16086_1:N:0:TTCCAAGG+CTACAAGG	NC_082383.1	1
Processed 6000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1196:35643:8074_1:N:0:TTCCAAGG+CTACAAGG	NC_082399.1	21077814
Processed 7000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1210:12143:13201_1:N:0:TTCCAAGG+CTACAAGG	NC_082399.1	21077818
Processed 8000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1222:3751:28707_1:N:0:TTCCAAGG+CTACAAGG	NC_082396.1	24646073
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1230:18536:18664_1:N:0:TTCCAAGG+CTACAAGG	NC_036931.1	1
Processed 9000000 sequence pairs so far
Processed 10000000 sequence pairs so far