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/EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz
../../data/EF05-EM06-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/EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz and ../../data/EF05-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz
Input files are in FastQ format
Writing a C -> T converted version of the input file EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz to EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz to EF05-EM06-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 EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz (198770863 sequences in total)

Writing a C -> T converted version of the input file EF05-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz to EF05-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file EF05-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz to EF05-EM06-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 EF05-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz (198770863 sequences in total)

Input files are EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz_C_to_T.fastq and EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz_G_to_A.fastq and EF05-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz_C_to_T.fastq and EF05-EM06-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 EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz_C_to_T.fastq and EF05-EM06-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:GW210315000:4:1101:26630:1047_1:N:0:TTACAGGA+GCTTGTCA/1	77	*	0	0	*	*	0	0	ANTATAATAAAAATTTTTTTATTAATATTAATATTAATAAAATTATAATTTTAAATATTTTAATTAAAATATATTAATAAATTATTTTATTATTTTATTATTTAAATTTATGG	F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF	YT:Z:UP
GWNJ-1012:512:GW210315000:4:1101:26630:1047_2:N:0:TTACAGGA+GCTTGTCA/2	141	*	0	0	*	*	0	0	CCATAAATTTAAATAATAAAATAATAAAATAATTTATTAATATATTTTAATTAAAATATTTAAAATTATAATTTTATTAATATTAATATTAATAAAAAAATTTTTATTATAAT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz_G_to_A.fastq and EF05-EM06-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:GW210315000:4:1101:26630:1047_1:N:0:TTACAGGA+GCTTGTCA/1	99	NC_035784.1_GA_converted	20135244	1	113M	=	20135244	113	ANTATAATAAAAACCCCTCCATTAATATTAACATTAATAAAATCACAACTCTAAACATTTCAACTAAAACACACCAACAAACTACTTTATTACTTTATTATCTAAACCTACAA	F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF	AS:i:-13	XS:i:-13	XN:i:0	XM:i:3	XO:i:0	XG:i:0	NM:i:3	MD:Z:1T108T1T0	YS:i:-12	YT:Z:CP
GWNJ-1012:512:GW210315000:4:1101:26630:1047_2:N:0:TTACAGGA+GCTTGTCA/2	147	NC_035784.1_GA_converted	20135244	1	113M	=	20135244	-113	ATTATAATAAAAACCCCTCCATTAATATTAACATTAATAAAATCACAACTCTAAACATTTCAACTAAAACACACCAACAAACTACTTTATTACTTTATTATCTAAACCTACAA	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FF:FFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	AS:i:-12	XS:i:-12	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:110T1T0	YS:i:-13	YT:Z:CP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz_G_to_A.fastq and EF05-EM06-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:GW210315000:4:1101:26630:1047_1:N:0:TTACAGGA+GCTTGTCA/1	77	*	0	0	*	*	0	0	ANTATAATAAAAACCCCTCCATTAATATTAACATTAATAAAATCACAACTCTAAACATTTCAACTAAAACACACCAACAAACTACTTTATTACTTTATTATCTAAACCTACAA	F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF	YT:Z:UP
GWNJ-1012:512:GW210315000:4:1101:26630:1047_2:N:0:TTACAGGA+GCTTGTCA/2	141	*	0	0	*	*	0	0	TTGTAGGTTTAGATAATAAAGTAATAAAGTAGTTTGTTGGTGTGTTTTAGTTGAAATGTTTAGAGTTGTGATTTTATTAATGTTAATATTAATGGAGGGGTTTTTATTATAAT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz_C_to_T.fastq and EF05-EM06-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:GW210315000:4:1101:26630:1047_1:N:0:TTACAGGA+GCTTGTCA/1	77	*	0	0	*	*	0	0	ANTATAATAAAAATTTTTTTATTAATATTAATATTAATAAAATTATAATTTTAAATATTTTAATTAAAATATATTAATAAATTATTTTATTATTTTATTATTTAAATTTATGG	F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF	YT:Z:UP
GWNJ-1012:512:GW210315000:4:1101:26630:1047_2:N:0:TTACAGGA+GCTTGTCA/2	141	*	0	0	*	*	0	0	CCATAAATTTAAATAATAAAATAATAAAATAATTTATTAATATATTTTAATTAAAATATTTAAAATTATAATTTTATTAATATTAATATTAATAAAAAAATTTTTATTATAAT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	YT:Z:UP

>>> Writing bisulfite mapping results to EF05-EM06-Larvae_pe.bam <<<


Reading in the sequence files ../../data/EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz and ../../data/EF05-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz
Processed 1000000 sequence pairs so far
Processed 2000000 sequence pairs so far
Processed 3000000 sequence pairs so far
Processed 4000000 sequence pairs so far
Processed 5000000 sequence pairs so far
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Processed 7000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:1234:3586:1689_1:N:0:TTACAGGA+GCTTGTCA	NC_007175.2	17121
Processed 8000000 sequence pairs so far
Processed 9000000 sequence pairs so far
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Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:1432:20446:13573_1:N:0:TTACAGGA+GCTTGTCA	NC_007175.2	1
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:1432:20582:21981_1:N:0:TTACAGGA+GCTTGTCA	NC_007175.2	1
Processed 18000000 sequence pairs so far
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Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:1677:32027:21136_1:N:0:TTACAGGA+GCTTGTCA	NC_035780.1	2
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:1677:31855:21339_1:N:0:TTACAGGA+GCTTGTCA	NC_035780.1	2
Processed 32000000 sequence pairs so far
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Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2251:28971:18192_1:N:0:TTACAGGA+GCTTGTCA	NC_035780.1	2
Processed 40000000 sequence pairs so far
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