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-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz
../../data/CF08-CM03-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/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-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz and ../../data/CF08-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz
Input files are in FastQ format
Writing a C -> T converted version of the input file CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz to CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz to CF08-CM03-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 CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz (147000143 sequences in total)

Writing a C -> T converted version of the input file CF08-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz to CF08-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file CF08-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz to CF08-CM03-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 CF08-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz (147000143 sequences in total)

Input files are CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz_C_to_T.fastq and CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz_G_to_A.fastq and CF08-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz_C_to_T.fastq and CF08-CM03-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,-0.8 -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-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz_C_to_T.fastq and CF08-CM03-Zygote_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:GW210315000:4:1101:28619:1047_1:N:0:GACCTGAA+CTCACCAA/1	77	*	0	0	*	*	0	0	GNGTAGTTTATTATGATGGAATAGGTTAATGTAGGAATGTGTGTAGTTTGTTGGT	F#F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF,FF	YT:Z:UP
GWNJ-1012:512:GW210315000:4:1101:28619:1047_2:N:0:GACCTGAA+CTCACCAA/2	141	*	0	0	*	*	0	0	ACCAACAAACTACACACATTCCTACATTAACCTATTCCATCATAATAAACTACCC	FFFFFFFFFFFFFFFFFFFFFFFFF:::FFFFFFFFFF:FFFFFFFFFFFFFFFF	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz_G_to_A.fastq and CF08-CM03-Zygote_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:GW210315000:4:1101:28619:1047_1:N:0:GACCTGAA+CTCACCAA/1	77	*	0	0	*	*	0	0	ANATAATTTATTATAATAAAATAAATTAATATAAAAATATATATAATTTATTAAT	F#F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF,FF	YT:Z:UP
GWNJ-1012:512:GW210315000:4:1101:28619:1047_2:N:0:GACCTGAA+CTCACCAA/2	141	*	0	0	*	*	0	0	ATTAATAAATTATATATATTTTTATATTAATTTATTTTATTATAATAAATTATTT	FFFFFFFFFFFFFFFFFFFFFFFFF:::FFFFFFFFFF:FFFFFFFFFFFFFFFF	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz_G_to_A.fastq and CF08-CM03-Zygote_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:GW210315000:4:1101:28619:1047_1:N:0:GACCTGAA+CTCACCAA/1	77	*	0	0	*	*	0	0	ANATAATTTATTATAATAAAATAAATTAATATAAAAATATATATAATTTATTAAT	F#F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF,FF	YT:Z:UP
GWNJ-1012:512:GW210315000:4:1101:28619:1047_2:N:0:GACCTGAA+CTCACCAA/2	141	*	0	0	*	*	0	0	ATTAATAAATTATATATATTTTTATATTAATTTATTTTATTATAATAAATTATTT	FFFFFFFFFFFFFFFFFFFFFFFFF:::FFFFFFFFFF:FFFFFFFFFFFFFFFF	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz_C_to_T.fastq and CF08-CM03-Zygote_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:GW210315000:4:1101:28619:1047_1:N:0:GACCTGAA+CTCACCAA/1	77	*	0	0	*	*	0	0	GNGTAGTTTATTATGATGGAATAGGTTAATGTAGGAATGTGTGTAGTTTGTTGGT	F#F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF,FF	YT:Z:UP
GWNJ-1012:512:GW210315000:4:1101:28619:1047_2:N:0:GACCTGAA+CTCACCAA/2	141	*	0	0	*	*	0	0	ACCAACAAACTACACACATTCCTACATTAACCTATTCCATCATAATAAACTACCC	FFFFFFFFFFFFFFFFFFFFFFFFF:::FFFFFFFFFF:FFFFFFFFFFFFFFFF	YT:Z:UP

>>> Writing bisulfite mapping results to CF08-CM03-Zygote_pe.bam <<<


Reading in the sequence files ../../data/CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz and ../../data/CF08-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:1101:30969:27946_1:N:0:GACCTGAA+CTCACCAA	NC_007175.2	17132
Processed 1000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:1125:14986:4460_1:N:0:GACCTGAA+CTCACCAA	NC_007175.2	17166
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
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:1210:31467:1407_1:N:0:GACCTGAA+CTCACCAA	NC_007175.2	17161
Processed 7000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:1219:15383:22999_1:N:0:GACCTGAA+CTCACCAA	NC_007175.2	17169
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:1219:17626:24001_1:N:0:GACCTGAA+CTCACCAA	NC_007175.2	17169
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
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:1406:10710:33254_1:N:0:GACCTGAA+CTCACCAA	NC_007175.2	17164
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:1406:10420:33411_1:N:0:GACCTGAA+CTCACCAA	NC_007175.2	17164
Processed 18000000 sequence pairs so far
Processed 19000000 sequence pairs so far
Processed 20000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:1453:18132:6464_1:N:0:GACCTGAA+CTCACCAA	NC_007175.2	17151
Processed 21000000 sequence pairs so far
Processed 22000000 sequence pairs so far
Processed 23000000 sequence pairs so far
Processed 24000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:1522:25409:20447_1:N:0:GACCTGAA+CTCACCAA	NC_007175.2	2
Processed 25000000 sequence pairs so far
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
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:1656:32325:32612_1:N:0:GACCTGAA+CTCACCAA	NC_007175.2	17149
Processed 33000000 sequence pairs so far
Processed 34000000 sequence pairs so far
Processed 35000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2124:28221:25661_1:N:0:GACCTGAA+CTCACCAA	NC_007175.2	17107
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2135:4363:6355_1:N:0:GACCTGAA+CTCACCAA	NC_007175.2	17178
Processed 36000000 sequence pairs so far
Processed 37000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2152:32777:14669_1:N:0:GACCTGAA+CTCACCAA	NC_007175.2	17151
Processed 38000000 sequence pairs so far
Processed 39000000 sequence pairs so far
Processed 40000000 sequence pairs so far
Processed 41000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2240:26142:3991_1:N:0:GACCTGAA+CTCACCAA	NC_007175.2	17161
Processed 42000000 sequence pairs so far
Processed 43000000 sequence pairs so far
Processed 44000000 sequence pairs so far
Processed 45000000 sequence pairs so far
Processed 46000000 sequence pairs so far
Processed 47000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2343:27019:35665_1:N:0:GACCTGAA+CTCACCAA	NC_007175.2	17151
Processed 48000000 sequence pairs so far
Processed 49000000 sequence pairs so far
Processed 50000000 sequence pairs so far
Processed 51000000 sequence pairs so far
Processed 52000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2432:15835:27884_1:N:0:GACCTGAA+CTCACCAA	NC_007175.2	17152
Processed 53000000 sequence pairs so far
Processed 54000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2467:22905:30514_1:N:0:GACCTGAA+CTCACCAA	NC_035780.1	65668291
Processed 55000000 sequence pairs so far
Processed 56000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2520:23936:35744_1:N:0:GACCTGAA+CTCACCAA	NC_007175.2	2
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2521:18132:1141_1:N:0:GACCTGAA+CTCACCAA	NC_007175.2	2
Processed 57000000 sequence pairs so far
Processed 58000000 sequence pairs so far
Processed 59000000 sequence pairs so far
Processed 60000000 sequence pairs so far
Processed 61000000 sequence pairs so far
Processed 62000000 sequence pairs so far
Processed 63000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2630:21522:15374_1:N:0:GACCTGAA+CTCACCAA	NC_007175.2	2
Processed 64000000 sequence pairs so far
Processed 65000000 sequence pairs so far
Processed 66000000 sequence pairs so far
Processed 67000000 sequence pairs so far
Processed 68000000 sequence pairs so far
Processed 69000000 sequence pairs so far
Processed 70000000 sequence pairs so far
Processed 71000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1013:195:GW2105211192nd:2:1155:2573:27117_1:N:0:GACCTGAA+CTCACCAA	NC_007175.2	17174
Processed 72000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1013:195:GW2105211192nd:2:1173:24207:17989_1:N:0:GACCTGAA+CTCACCAA	NC_007175.2	2
Processed 73000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1013:195:GW2105211192nd:2:1203:3188:27117_1:N:0:GACCTGAA+CTCACCAA	NC_007175.2	17179
Chromosomal sequence could not be extracted for	GWNJ-1013:195:GW2105211192nd:2:1211:4426:18771_1:N:0:GACCTGAA+CTCACCAA	NC_007175.2	2
Processed 74000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1013:195:GW2105211192nd:2:1213:21658:4053_1:N:0:GACCTGAA+CTCACCAA	NC_007175.2	2
Processed 75000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1013:195:GW2105211192nd:2:1228:19461:25207_1:N:0:GACCTGAA+CTCACCAA	NC_007175.2	1
Chromosomal sequence could not be extracted for	GWNJ-1013:195:GW2105211192nd:2:1228:19190:25895_1:N:0:GACCTGAA+CTCACCAA	NC_007175.2	1
Processed 76000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1013:195:GW2105211192nd:2:1240:18548:32268_1:N:0:GACCTGAA+CTCACCAA	NC_007175.2	2
Processed 77000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1013:195:GW2105211192nd:2:1252:25626:36761_1:N:0:GACCTGAA+CTCACCAA	NC_007175.2	17175
Processed 78000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1013:195:GW2105211192nd:2:1259:20735:18521_1:N:0:GACCTGAA+CTCACCAA	NC_007175.2	17132
Chromosomal sequence could not be extracted for	GWNJ-1013:195:GW2105211192nd:2:1261:15103:1783_1:N:0:GACCTGAA+CTCACCAA	NC_007175.2	17132
Processed 79000000 sequence pairs so far