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)
Processing sequences up to read no. 10000 from the input file
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/04-bismark-align'):
../../data/CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz
../../data/CF07-CM02-Zygote_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/04-bismark-align/
Setting parallelization to single-threaded (default)

Summary of all aligner options:	-q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500
Current working directory is: /mmfs1/gscratch/scrubbed/sr320/github/ceasmallr/output/04-bismark-align

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/CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz and ../../data/CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz
Input files are in FastQ format
Processing reads up to sequence no. 10000 from ../../data/CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz
Writing a C -> T converted version of the input file CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz to CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz to CF07-CM02-Zygote_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 CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz (10001 sequences in total)

Processing reads up to sequence no. 10000 from ../../data/CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz
Writing a C -> T converted version of the input file CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz to CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz to CF07-CM02-Zygote_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 CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz (10001 sequences in total)

Input files are CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz_C_to_T.fastq and CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz_G_to_A.fastq and CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz_C_to_T.fastq and CF07-CM02-Zygote_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,-0.6 -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 CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz_C_to_T.fastq and CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc))
Found first alignment:
GWNJ-1012:512:GW210315000:4:1101:26594:1047_1:N:0:AGTACCTT+GACGTCTT/1	77	*	0	0	*	*	0	0	TNTGGAATTTATTGAGTGAAAGTGTGGATGTAGTTTGTTGTTTAATTTTATTTGTGGTAATGTTGTGTAGATGTTTTGGTATGTAATAATGTTTATTATTTTTATTTTTTTGGGGTTGGATGGTATGATATTGTTGTGTGAATATGTTGG	F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	YT:Z:UP
GWNJ-1012:512:GW210315000:4:1101:26594:1047_2:N:0:AGTACCTT+GACGTCTT/2	141	*	0	0	*	*	0	0	ACTACCACCACCATAATAACCAACATATTCACACAACAATATCATACCATCCAACCCCAAAAAAATAAAAATAATAAACATTATTACATACCAAAACATCTACACAACATTACCACAAATAAAATTAAACAACAAACTACATCCACACTT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz_G_to_A.fastq and CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc))
Found first alignment:
GWNJ-1012:512:GW210315000:4:1101:26594:1047_1:N:0:AGTACCTT+GACGTCTT/1	77	*	0	0	*	*	0	0	TNTAAAATTTATTAAATAAAAATATAAATATAATTTATTATTTAATTTTATTTATAATAATATTATATAAATATTTTAATATATAATAATATTTATTATTTTTATTTTTTTAAAATTAAATAATATAATATTATTATATAAATATATTAA	F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	YT:Z:UP
GWNJ-1012:512:GW210315000:4:1101:26594:1047_2:N:0:AGTACCTT+GACGTCTT/2	141	*	0	0	*	*	0	0	ATTATTATTATTATAATAATTAATATATTTATATAATAATATTATATTATTTAATTTTAAAAAAATAAAAATAATAAATATTATTATATATTAAAATATTTATATAATATTATTATAAATAAAATTAAATAATAAATTATATTTATATTT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz_G_to_A.fastq and CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw))
Found first alignment:
GWNJ-1012:512:GW210315000:4:1101:26594:1047_1:N:0:AGTACCTT+GACGTCTT/1	77	*	0	0	*	*	0	0	TNTAAAATTTATTAAATAAAAATATAAATATAATTTATTATTTAATTTTATTTATAATAATATTATATAAATATTTTAATATATAATAATATTTATTATTTTTATTTTTTTAAAATTAAATAATATAATATTATTATATAAATATATTAA	F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	YT:Z:UP
GWNJ-1012:512:GW210315000:4:1101:26594:1047_2:N:0:AGTACCTT+GACGTCTT/2	141	*	0	0	*	*	0	0	ATTATTATTATTATAATAATTAATATATTTATATAATAATATTATATTATTTAATTTTAAAAAAATAAAAATAATAAATATTATTATATATTAAAATATTTATATAATATTATTATAAATAAAATTAAATAATAAATTATATTTATATTT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz_C_to_T.fastq and CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw))
Found first alignment:
GWNJ-1012:512:GW210315000:4:1101:26594:1047_1:N:0:AGTACCTT+GACGTCTT/1	77	*	0	0	*	*	0	0	TNTGGAATTTATTGAGTGAAAGTGTGGATGTAGTTTGTTGTTTAATTTTATTTGTGGTAATGTTGTGTAGATGTTTTGGTATGTAATAATGTTTATTATTTTTATTTTTTTGGGGTTGGATGGTATGATATTGTTGTGTGAATATGTTGG	F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	YT:Z:UP
GWNJ-1012:512:GW210315000:4:1101:26594:1047_2:N:0:AGTACCTT+GACGTCTT/2	141	*	0	0	*	*	0	0	ACTACCACCACCATAATAACCAACATATTCACACAACAATATCATACCATCCAACCCCAAAAAAATAAAAATAATAAACATTATTACATACCAAAACATCTACACAACATTACCACAAATAAAATTAAACAACAAACTACATCCACACTT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF	YT:Z:UP

>>> Writing bisulfite mapping results to CF07-CM02-Zygote_pe.bam <<<


Reading in the sequence files ../../data/CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz and ../../data/CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz
1000010000 reads; of these: reads; of these:

    1000010000 ( (100.00100.00%%) were paired; of these:) were paired; of these:

        94299436 ( (94.2994.36%%) aligned concordantly 0 times) aligned concordantly 0 times

        256257 ( (2.562.57%%) aligned concordantly exactly 1 time) aligned concordantly exactly 1 time

        315307 ( (3.153.07%%) aligned concordantly >1 times) aligned concordantly >1 times

5.715.64%% overall alignment rate overall alignment rate

10000 reads; of these:
  10000 (100.00%10000) were paired; of these: reads; of these:

      934710000 ( (93.47%) aligned concordantly 0 times100.00
%    ) were paired; of these:308
 (    3.089404% () aligned concordantly exactly 1 time94.04
%    ) aligned concordantly 0 times345
 (    3.45274% () aligned concordantly >1 times2.74
%6.53) aligned concordantly exactly 1 time%
 overall alignment rate    
322 (3.22%) aligned concordantly >1 times
5.96% overall alignment rate
Processed 10000 sequences in total


Successfully deleted the temporary files CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz_C_to_T.fastq, CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz_G_to_A.fastq, CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz_C_to_T.fastq and CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz_G_to_A.fastq

Final Alignment report
======================
Sequence pairs analysed in total:	10000
Final Cytosine Methylation Report
=================================
Total number of C's analysed:	35128

Total methylated C's in CpG context:	921
Total methylated C's in CHG context:	168
Total methylated C's in CHH context:	1050
Total methylated C's in Unknown context:	53

Total unmethylated C's in CpG context:	3670
Total unmethylated C's in CHG context:	6935
Total unmethylated C's in CHH context:	22384
Total unmethylated C's in Unknown context:	185

C methylated in CpG context:	20.1%
C methylated in CHG context:	2.4%
C methylated in CHH context:	4.5%
C methylated in Unknown context (CN or CHN):	22.3%


Bismark completed in 0d 0h 0m 15s

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