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/CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz
../../data/CF08-CM04-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/CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz and ../../data/CF08-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz
Input files are in FastQ format
Writing a C -> T converted version of the input file CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz to CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz to CF08-CM04-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 CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz (53999416 sequences in total)

Writing a C -> T converted version of the input file CF08-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz to CF08-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file CF08-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz to CF08-CM04-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 CF08-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz (53999416 sequences in total)

Input files are CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz_C_to_T.fastq and CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz_G_to_A.fastq and CF08-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz_C_to_T.fastq and CF08-CM04-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 CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz_C_to_T.fastq and CF08-CM04-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:GW210315000:4:1101:26847:1047_1:N:0:GGCATTCT+CAAGCTAG/1	77	*	0	0	*	*	0	0	TNATTATTTTTTGTAATTTGGTTATGTTGGTATGAGATTGTGAATTGTTAATTAAGTAGGGGTATTAGTTAAGTAAATTGGGGT	F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFF:FFF	YT:Z:UP
GWNJ-1012:512:GW210315000:4:1101:26847:1047_2:N:0:GGCATTCT+CAAGCTAG/2	141	*	0	0	*	*	0	0	ACCCCAATTTACTTAACTAATACCCCTACTTAATTAACAATTCACAATCTCATACCAACATAACCAAATTACAAAAAATAATTA	FFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFF:FFFFFFFFFFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz_G_to_A.fastq and CF08-CM04-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:GW210315000:4:1101:26847:1047_1:N:0:GGCATTCT+CAAGCTAG/1	77	*	0	0	*	*	0	0	CNACTATTTTTTATAATTTAATTATATTAATATAAAATTATAAATTATTAATTAAATAAAAATATTAATTAAATAAATTAAAAC	F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFF:FFF	YT:Z:UP
GWNJ-1012:512:GW210315000:4:1101:26847:1047_2:N:0:GGCATTCT+CAAGCTAG/2	141	*	0	0	*	*	0	0	GTTTTAATTTATTTAATTAATATTTTTATTTAATTAATAATTTATAATTTTATATTAATATAATTAAATTATAAAAAATAGTTG	FFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFF:FFFFFFFFFFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz_G_to_A.fastq and CF08-CM04-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:GW210315000:4:1101:26847:1047_1:N:0:GGCATTCT+CAAGCTAG/1	77	*	0	0	*	*	0	0	CNACTATTTTTTATAATTTAATTATATTAATATAAAATTATAAATTATTAATTAAATAAAAATATTAATTAAATAAATTAAAAC	F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFF:FFF	YT:Z:UP
GWNJ-1012:512:GW210315000:4:1101:26847:1047_2:N:0:GGCATTCT+CAAGCTAG/2	141	*	0	0	*	*	0	0	GTTTTAATTTATTTAATTAATATTTTTATTTAATTAATAATTTATAATTTTATATTAATATAATTAAATTATAAAAAATAGTTG	FFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFF:FFFFFFFFFFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz_C_to_T.fastq and CF08-CM04-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:GW210315000:4:1101:26847:1047_1:N:0:GGCATTCT+CAAGCTAG/1	77	*	0	0	*	*	0	0	TNATTATTTTTTGTAATTTGGTTATGTTGGTATGAGATTGTGAATTGTTAATTAAGTAGGGGTATTAGTTAAGTAAATTGGGGT	F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFF:FFF	YT:Z:UP
GWNJ-1012:512:GW210315000:4:1101:26847:1047_2:N:0:GGCATTCT+CAAGCTAG/2	141	*	0	0	*	*	0	0	ACCCCAATTTACTTAACTAATACCCCTACTTAATTAACAATTCACAATCTCATACCAACATAACCAAATTACAAAAAATAATTA	FFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFF:FFFFFFFFFFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	YT:Z:UP

>>> Writing bisulfite mapping results to CF08-CM04-Larvae_pe.bam <<<


Reading in the sequence files ../../data/CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz and ../../data/CF08-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz
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Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2203:20139:18427_1:N:0:GGCATTCT+CAAGCTAG	NC_007175.2	17120
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Processed 53000000 sequence pairs so far
53999416 reads; of these:
  53999416 (100.00%) were paired; of these:
    53454808 (98.99%) aligned concordantly 0 times
    213985 (0.40%) aligned concordantly exactly 1 time
    330623 (0.61%) aligned concordantly >1 times
1.01% overall alignment rate
53999416 reads; of these:
  53999416 (100.00%) were paired; of these:
    53534706 (99.14%) aligned concordantly 0 times
    182251 (0.34%) aligned concordantly exactly 1 time
    282459 (0.52%) aligned concordantly >1 times
0.86% overall alignment rate
53999416 reads; of these:
  53999416 (100.00%) were paired; of these:
    53535657 (99.14%) aligned concordantly 0 times
    181515 (0.34%) aligned concordantly exactly 1 time
    282244 (0.52%) aligned concordantly >1 times
0.86% overall alignment rate
53999416 reads; of these:
  53999416 (100.00%) were paired; of these:
    53455173 (98.99%) aligned concordantly 0 times
    213042 (0.39%) aligned concordantly exactly 1 time
    331201 (0.61%) aligned concordantly >1 times
1.01% overall alignment rate
Processed 53999416 sequences in total


Successfully deleted the temporary files CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz_C_to_T.fastq, CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz_G_to_A.fastq, CF08-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz_C_to_T.fastq and CF08-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz_G_to_A.fastq

Final Alignment report
======================
Sequence pairs analysed in total:	53999416
Final Cytosine Methylation Report
=================================
Total number of C's analysed:	27190456

Total methylated C's in CpG context:	517560
Total methylated C's in CHG context:	184091
Total methylated C's in CHH context:	4365052
Total methylated C's in Unknown context:	195586

Total unmethylated C's in CpG context:	2239687
Total unmethylated C's in CHG context:	3887850
Total unmethylated C's in CHH context:	15996216
Total unmethylated C's in Unknown context:	285413

C methylated in CpG context:	18.8%
C methylated in CHG context:	4.5%
C methylated in CHH context:	21.4%
C methylated in Unknown context (CN or CHN):	40.7%


Bismark completed in 0d 2h 0m 1s

====================
Bismark run complete
====================