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/01B_1.fastq.gz
/mmfs1/gscratch/coenv/sr320/cod-bs/01B_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/01B_1.fastq.gz and /mmfs1/gscratch/coenv/sr320/cod-bs/01B_2.fastq.gz
Input files are in FastQ format
Writing a C -> T converted version of the input file 01B_1.fastq.gz to 01B_1.fastq.gz_C_to_T.fastq

Created C -> T converted version of the FastQ file 01B_1.fastq.gz (54782946 sequences in total)

Writing a G -> A converted version of the input file 01B_2.fastq.gz to 01B_2.fastq.gz_G_to_A.fastq

Created G -> A converted version of the FastQ file 01B_2.fastq.gz (54782946 sequences in total)

Input files are 01B_1.fastq.gz_C_to_T.fastq and 01B_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 01B_1.fastq.gz_C_to_T.fastq and 01B_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:
LH00160:538:22WG5VLT4:6:1101:22372:1042_1:N:0:CTGATCGT+GCNCATAT/1	77	*	0	0	*	*	0	0	GNGTTTTTTTATTGTTGTAAATTAGTTTAGGAGAGATTGGTGATTTTGTTTAGGATATGTGTTAATTTAGTTTAGGTTTAGTGTTGTTGAGTAGGTAGTTTATGAAAATGGTTTTTTTAAGTGTATGTGTGTGTGTATGTGAGTGTGTGTG	I#IIIIIIIIIIIIIIII9IIII-IIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-9IIIIII-I9IIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UP
LH00160:538:22WG5VLT4:6:1101:22372:1042_2:N:0:CTGATCGT+GCNCATAT/2	141	*	0	0	*	*	0	0	AAAAAAACACACACACACTCACATACACACACACATACACTTAAAAAAACCATTTTCATAAACTACCTACTCAACAACACTAAACCTAAACTAAATTAACACATATCCTAAACAAAATCACCAATCTCTCATAAACTAATTTACAACAATA	99-9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-II-II9IIIIIIIIIIIIII-IIIIIIIIIIII9IIIII--	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 01B_1.fastq.gz_C_to_T.fastq and 01B_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:
LH00160:538:22WG5VLT4:6:1101:22372:1042_1:N:0:CTGATCGT+GCNCATAT/1	83	NC_082394.1_GA_converted	17244784	42	151M	=	17244775	-160	CACACACACTCACATACACACACACATACACTTAAAAAAACCATTTTCATAAACTACCTACTCAACAACACTAAACCTAAACTAAATTAACACATATCCTAAACAAAATCACCAATCTCTCCTAAACTAATTTACAACAATAAAAAAACNC	IIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIII9I-IIIIII9-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIII-IIII9IIIIIIIIIIIIIIII#I	AS:i:-1	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:149A1	YS:i:-24	YT:Z:CP
LH00160:538:22WG5VLT4:6:1101:22372:1042_2:N:0:CTGATCGT+GCNCATAT/2	163	NC_082394.1_GA_converted	17244775	42	151M	=	17244784	160	AAAAAAACACACACACACTCACATACACACACACATACACTTAAAAAAACCATTTTCATAAACTACCTACTCAACAACACTAAACCTAAACTAAATTAACACATATCCTAAACAAAATCACCAATCTCTCATAAACTAATTTACAACAATA	99-9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-II-II9IIIIIIIIIIIIII-IIIIIIIIIIII9IIIII--	AS:i:-24	XN:i:0	XM:i:4	XO:i:0	XG:i:0	NM:i:4	MD:Z:1C1C1C124C20	YS:i:-1	YT:Z:CP

>>> Writing bisulfite mapping results to 01B_pe.bam <<<


Reading in the sequence files /mmfs1/gscratch/coenv/sr320/cod-bs/01B_1.fastq.gz and /mmfs1/gscratch/coenv/sr320/cod-bs/01B_2.fastq.gz
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1113:13899:9321_1:N:0:CTGATCGT+GCGCATAT	NC_082399.1	21077814
Processed 1000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1133:46252:10021_1:N:0:CTGATCGT+GCGCATAT	NC_082399.1	21077814
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1135:28449:25766_1:N:0:CTGATCGT+GCGCATAT	NC_082382.1	1
Processed 2000000 sequence pairs so far
Processed 3000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1175:21789:3115_1:N:0:CTGATCGT+GCGCATAT	NC_082382.1	26289605
Processed 4000000 sequence pairs so far
Processed 5000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1206:19127:19378_1:N:0:CTGATCGT+GCGCATAT	NC_082393.1	1
Processed 6000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1231:2351:4824_1:N:0:CTGATCGT+GCGCATAT	NC_082394.1	22312310
Processed 7000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1258:29185:4376_1:N:0:CTGATCGT+GCGCATAT	NC_082384.1	1
Processed 8000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1271:26928:14027_1:N:0:CTGATCGT+GCGCATAT	NC_082395.1	3
Processed 9000000 sequence pairs so far
Processed 10000000 sequence pairs so far
Processed 11000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1330:47101:27209_1:N:0:CTGATCGT+GCGCATAT	NC_082387.1	1
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1333:42602:2779_1:N:0:CTGATCGT+GCGCATAT	NC_036931.1	16421
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1333:19021:28777_1:N:0:CTGATCGT+GCGCATAT	NC_082387.1	1
Processed 12000000 sequence pairs so far
Processed 13000000 sequence pairs so far
Chromosomal sequence could not be extracted for	LH00160:538:22WG5VLT4:6:1368:46041:28651_1:N:0:CTGATCGT+GCGCATAT	NC_082399.1	21077814
Processed 14000000 sequence pairs so far