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 ../../data/genome/	(absolute path is '/mmfs1/gscratch/scrubbed/sr320/github/ceasmallr/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/ceasmallr/output/05-bismark-align-full'):
../../data/EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz
../../data/EF06-EM02-Larvae_R2_001.fastp-trim.20220827.fq.gz
Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported
Output will be written into the directory: /mmfs1/gscratch/scrubbed/sr320/github/ceasmallr/output/05-bismark-align-full/
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/ceasmallr/output/05-bismark-align-full

Now reading in and storing sequence information of the genome specified in: /mmfs1/gscratch/scrubbed/sr320/github/ceasmallr/data/genome/

Single-core mode: setting pid to 1

Paired-end alignments will be performed
=======================================

The provided filenames for paired-end alignments are ../../data/EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz and ../../data/EF06-EM02-Larvae_R2_001.fastp-trim.20220827.fq.gz
Input files are in FastQ format
Writing a C -> T converted version of the input file EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz to EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz to EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz_G_to_A.fastq

Created C -> T as well as G -> A converted versions of the FastQ file EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz (116122621 sequences in total)

Writing a C -> T converted version of the input file EF06-EM02-Larvae_R2_001.fastp-trim.20220827.fq.gz to EF06-EM02-Larvae_R2_001.fastp-trim.20220827.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file EF06-EM02-Larvae_R2_001.fastp-trim.20220827.fq.gz to EF06-EM02-Larvae_R2_001.fastp-trim.20220827.fq.gz_G_to_A.fastq

Created C -> T as well as G -> A converted versions of the FastQ file EF06-EM02-Larvae_R2_001.fastp-trim.20220827.fq.gz (116122621 sequences in total)

Input files are EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz_C_to_T.fastq and EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz_G_to_A.fastq and EF06-EM02-Larvae_R2_001.fastp-trim.20220827.fq.gz_C_to_T.fastq and EF06-EM02-Larvae_R2_001.fastp-trim.20220827.fq.gz_G_to_A.fastq (FastQ)
Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /mmfs1/gscratch/scrubbed/sr320/github/ceasmallr/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 EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz_C_to_T.fastq and EF06-EM02-Larvae_R2_001.fastp-trim.20220827.fq.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:
GWNJ-1012:512:GW210315000:4:1101:25581:1047_1:N:0:GCAGAATT+TGGCCGGT/1	77	*	0	0	*	*	0	0	ANAAATAAATTTTTATTTGTTATTGAAATAAATTAATTTTTTTTTTAGTGTTTTTGTATGGTAGAATATTGGTTTGTTTGTTGTGTTAATGGTGTATTTTGTATTTTTGGAGATAAATAGTATTATGTTTTTTTGGTATATTATGTGGGT	F#FFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFF,FFF:F:FFF,FF,FFF::F:FFFF::F,::F::F:F::FFFFFFFFF:FFFFFF:FFFFFFFFF:FF,FFFFFFFFFFFFFFF,FFFFFFFF:F:FFFFFF	YT:Z:UP
GWNJ-1012:512:GW210315000:4:1101:25581:1047_2:N:0:GCAGAATT+TGGCCGGT/2	141	*	0	0	*	*	0	0	CAATATCTATATAAAATTCACCACAACACAAACATTTTTAATTTAAAAAAAACCTTACCACACCTACACCATACCTTAAACTTTATAACCCACATAATATACCAAAAAAACATAATACTATTTATCTCCAAAAATACAAAATACACCATT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz_G_to_A.fastq and EF06-EM02-Larvae_R2_001.fastp-trim.20220827.fq.gz_C_to_T.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:
GWNJ-1012:512:GW210315000:4:1101:25581:1047_1:N:0:GCAGAATT+TGGCCGGT/1	77	*	0	0	*	*	0	0	ANAAACAAACCCTTACCCACTACCAAAACAAACTAACCCCCTCTTTAATATTTTTATATAATAAAATATTAACTTATTTATTATATTAATAATATATTTTATATTTTTAAAAATAAATAATATTATATTTTTTTAATATATTATATAAAT	F#FFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFF,FFF:F:FFF,FF,FFF::F:FFFF::F,::F::F:F::FFFFFFFFF:FFFFFF:FFFFFFFFF:FF,FFFFFFFFFFFFFFF,FFFFFFFF:F:FFFFFF	YT:Z:UP
GWNJ-1012:512:GW210315000:4:1101:25581:1047_2:N:0:GCAGAATT+TGGCCGGT/2	141	*	0	0	*	*	0	0	TAATATTTATATAAAATTTATTATAATATAAATATTTTTAATTTAAAAAAAATTTTATTATATTTATATTATATTTTAAATTTTATAATTTATATAATATATTAAAAAAATATAATATTATTTATTTTTAAAAATATAAAATATATTATT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz_G_to_A.fastq and EF06-EM02-Larvae_R2_001.fastp-trim.20220827.fq.gz_C_to_T.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:
GWNJ-1012:512:GW210315000:4:1101:25581:1047_1:N:0:GCAGAATT+TGGCCGGT/1	77	*	0	0	*	*	0	0	ANAAACAAACCCTTACCCACTACCAAAACAAACTAACCCCCTCTTTAATATTTTTATATAATAAAATATTAACTTATTTATTATATTAATAATATATTTTATATTTTTAAAAATAAATAATATTATATTTTTTTAATATATTATATAAAT	F#FFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFF,FFF:F:FFF,FF,FFF::F:FFFF::F,::F::F:F::FFFFFFFFF:FFFFFF:FFFFFFFFF:FF,FFFFFFFFFFFFFFF,FFFFFFFF:F:FFFFFF	YT:Z:UP
GWNJ-1012:512:GW210315000:4:1101:25581:1047_2:N:0:GCAGAATT+TGGCCGGT/2	141	*	0	0	*	*	0	0	TAATATTTATATAAAATTTATTATAATATAAATATTTTTAATTTAAAAAAAATTTTATTATATTTATATTATATTTTAAATTTTATAATTTATATAATATATTAAAAAAATATAATATTATTTATTTTTAAAAATATAAAATATATTATT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz_C_to_T.fastq and EF06-EM02-Larvae_R2_001.fastp-trim.20220827.fq.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:
GWNJ-1012:512:GW210315000:4:1101:25581:1047_1:N:0:GCAGAATT+TGGCCGGT/1	77	*	0	0	*	*	0	0	ANAAATAAATTTTTATTTGTTATTGAAATAAATTAATTTTTTTTTTAGTGTTTTTGTATGGTAGAATATTGGTTTGTTTGTTGTGTTAATGGTGTATTTTGTATTTTTGGAGATAAATAGTATTATGTTTTTTTGGTATATTATGTGGGT	F#FFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFF,FFF:F:FFF,FF,FFF::F:FFFF::F,::F::F:F::FFFFFFFFF:FFFFFF:FFFFFFFFF:FF,FFFFFFFFFFFFFFF,FFFFFFFF:F:FFFFFF	YT:Z:UP
GWNJ-1012:512:GW210315000:4:1101:25581:1047_2:N:0:GCAGAATT+TGGCCGGT/2	141	*	0	0	*	*	0	0	CAATATCTATATAAAATTCACCACAACACAAACATTTTTAATTTAAAAAAAACCTTACCACACCTACACCATACCTTAAACTTTATAACCCACATAATATACCAAAAAAACATAATACTATTTATCTCCAAAAATACAAAATACACCATT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F	YT:Z:UP

>>> Writing bisulfite mapping results to EF06-EM02-Larvae_pe.bam <<<


Reading in the sequence files ../../data/EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz and ../../data/EF06-EM02-Larvae_R2_001.fastp-trim.20220827.fq.gz
Processed 1000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:1131:6424:5228_1:N:0:GCAGAATT+TGGCCGGT	NC_035780.1	2
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:1131:6388:5259_1:N:0:GCAGAATT+TGGCCGGT	NC_035780.1	2
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
Processed 8000000 sequence pairs so far
Processed 9000000 sequence pairs so far
Processed 10000000 sequence pairs so far
Processed 11000000 sequence pairs so far
Processed 12000000 sequence pairs so far
Processed 13000000 sequence pairs so far
Processed 14000000 sequence pairs so far
Processed 15000000 sequence pairs so far
Processed 16000000 sequence pairs so far
Processed 17000000 sequence pairs so far
Processed 18000000 sequence pairs so far
Processed 19000000 sequence pairs so far
Processed 20000000 sequence pairs so far
Processed 21000000 sequence pairs so far
Processed 22000000 sequence pairs so far
Processed 23000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:1610:3631:10034_1:N:0:GCAGAATT+TGGCCGGT	NC_035780.1	2
Processed 24000000 sequence pairs so far
Processed 25000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:1646:19895:36636_1:N:0:GCAGAATT+TGGCCGGT	NC_035781.1	2
Processed 26000000 sequence pairs so far
Processed 27000000 sequence pairs so far
Processed 28000000 sequence pairs so far
Processed 29000000 sequence pairs so far
Processed 30000000 sequence pairs so far
Processed 31000000 sequence pairs so far
Processed 32000000 sequence pairs so far
Processed 33000000 sequence pairs so far
Processed 34000000 sequence pairs so far
Processed 35000000 sequence pairs so far
Processed 36000000 sequence pairs so far
Processed 37000000 sequence pairs so far
Processed 38000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2346:22372:15937_1:N:0:GCAGAATT+TGGCCGGT	NC_035781.1	2
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2349:31376:22263_1:N:0:GCAGAATT+TGGCCGGT	NC_007175.2	3
Processed 39000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2360:20247:6684_1:N:0:GCAGAATT+TGGCCGGT	NC_035781.1	3
Processed 40000000 sequence pairs so far
Processed 41000000 sequence pairs so far
Processed 42000000 sequence pairs so far
Processed 43000000 sequence pairs so far
Processed 44000000 sequence pairs so far
Processed 45000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2509:7111:23046_1:N:0:GCAGAATT+TGGCCGGT	NC_035781.1	3
Processed 46000000 sequence pairs so far
Processed 47000000 sequence pairs so far
Processed 48000000 sequence pairs so far
Processed 49000000 sequence pairs so far
Processed 50000000 sequence pairs so far
Processed 51000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2645:9968:35196_1:N:0:GCAGAATT+TGGCCGGT	NC_035780.1	2
Processed 52000000 sequence pairs so far
Processed 53000000 sequence pairs so far