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-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz
../../data/EF05-EM05-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/EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz and ../../data/EF05-EM05-Zygote_R2_001.fastp-trim.20220827.fq.gz
Input files are in FastQ format
Writing a C -> T converted version of the input file EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz to EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz to EF05-EM05-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 EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz (121477726 sequences in total)

Writing a C -> T converted version of the input file EF05-EM05-Zygote_R2_001.fastp-trim.20220827.fq.gz to EF05-EM05-Zygote_R2_001.fastp-trim.20220827.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file EF05-EM05-Zygote_R2_001.fastp-trim.20220827.fq.gz to EF05-EM05-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 EF05-EM05-Zygote_R2_001.fastp-trim.20220827.fq.gz (121477726 sequences in total)

Input files are EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz_C_to_T.fastq and EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz_G_to_A.fastq and EF05-EM05-Zygote_R2_001.fastp-trim.20220827.fq.gz_C_to_T.fastq and EF05-EM05-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 EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz_C_to_T.fastq and EF05-EM05-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:GW210315000:4:1101:25545:1047_1:N:0:AAGTCCAA+TACTCATA/1	77	*	0	0	*	*	0	0	TNTTGATTATTATGAAGGTGATGTTTTTAAAAATTAAGTTTTGAAGAAGGGTAGTATTTAAAGTAGAAGGTTTTGGGGTGTGTGATATGAAATGAAGTATTGGTTGTAAGTGTGATTTTGGATTAGTTGTTAATGTGTTAATTGTGGGGG	F#:FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:,FFFFFFFFFFFFFFFFFFFFFFFFFF:	YT:Z:UP
GWNJ-1012:512:GW210315000:4:1101:25545:1047_2:N:0:AAGTCCAA+TACTCATA/2	141	*	0	0	*	*	0	0	TTTAACTTTAATAATATATAACAATTATAATCCTAAACAAAAACCCCCCACAATTAACACATTAACAACTAATCCAAAATCACACTTACAACCAATACTTCATTTCATATCACACACCCCAAAACCTTCTACTTTAAATACTACCCTTCT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz_G_to_A.fastq and EF05-EM05-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:GW210315000:4:1101:25545:1047_1:N:0:AAGTCCAA+TACTCATA/1	77	*	0	0	*	*	0	0	CNTTAATTATTATAAAAATAATATTTTTAAAAATTAAATTTTAAAAAAAAATAATATTTAAAATAAAAAATTTTAAAATATATAATATAAAATAAAATATTAATTATAAATATAATTCTAAATTAATTATTAATATATTAATTATAAAAA	F#:FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:,FFFFFFFFFFFFFFFFFFFFFFFFFF:	YT:Z:UP
GWNJ-1012:512:GW210315000:4:1101:25545:1047_2:N:0:AAGTCCAA+TACTCATA/2	141	*	0	0	*	*	0	0	TTTAATTTTAATAATATATAATAATTATAATTTTAAATAAAAATTTTTTATAATTAATATATTAATAATTAATTTAGAATTATATTTATAATTAATATTTTATTTTATATTATATATTTTAAAATTTTTTATTTTAAATATTATTTTTTT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz_G_to_A.fastq and EF05-EM05-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:GW210315000:4:1101:25545:1047_1:N:0:AAGTCCAA+TACTCATA/1	77	*	0	0	*	*	0	0	CNTTAATTATTATAAAAATAATATTTTTAAAAATTAAATTTTAAAAAAAAATAATATTTAAAATAAAAAATTTTAAAATATATAATATAAAATAAAATATTAATTATAAATATAATTCTAAATTAATTATTAATATATTAATTATAAAAA	F#:FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:,FFFFFFFFFFFFFFFFFFFFFFFFFF:	YT:Z:UP
GWNJ-1012:512:GW210315000:4:1101:25545:1047_2:N:0:AAGTCCAA+TACTCATA/2	141	*	0	0	*	*	0	0	TTTAATTTTAATAATATATAATAATTATAATTTTAAATAAAAATTTTTTATAATTAATATATTAATAATTAATTTAGAATTATATTTATAATTAATATTTTATTTTATATTATATATTTTAAAATTTTTTATTTTAAATATTATTTTTTT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz_C_to_T.fastq and EF05-EM05-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:GW210315000:4:1101:25545:1047_1:N:0:AAGTCCAA+TACTCATA/1	77	*	0	0	*	*	0	0	TNTTGATTATTATGAAGGTGATGTTTTTAAAAATTAAGTTTTGAAGAAGGGTAGTATTTAAAGTAGAAGGTTTTGGGGTGTGTGATATGAAATGAAGTATTGGTTGTAAGTGTGATTTTGGATTAGTTGTTAATGTGTTAATTGTGGGGG	F#:FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:,FFFFFFFFFFFFFFFFFFFFFFFFFF:	YT:Z:UP
GWNJ-1012:512:GW210315000:4:1101:25545:1047_2:N:0:AAGTCCAA+TACTCATA/2	141	*	0	0	*	*	0	0	TTTAACTTTAATAATATATAACAATTATAATCCTAAACAAAAACCCCCCACAATTAACACATTAACAACTAATCCAAAATCACACTTACAACCAATACTTCATTTCATATCACACACCCCAAAACCTTCTACTTTAAATACTACCCTTCT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	YT:Z:UP

>>> Writing bisulfite mapping results to EF05-EM05-Zygote_pe.bam <<<


Reading in the sequence files ../../data/EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz and ../../data/EF05-EM05-Zygote_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
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:1210:30870:24079_1:N:0:AAGTCCAA+TACTCATA	NC_007175.2	17123
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
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:1343:16152:7921_1:N:0:AAGTCCAA+TACTCATA	NC_007175.2	1
Processed 11000000 sequence pairs so far
Processed 12000000 sequence pairs so far
Processed 13000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:1416:6162:29356_1:N:0:AAGTCCAA+TACTCATA	NC_007175.2	17176
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:GW210315000:4:1523:12572:29465_1:N:0:AAGTCCAA+TACTCATA	NC_007175.2	17184
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
Processed 24000000 sequence pairs so far
Processed 25000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2123:12572:4100_1:N:0:AAGTCCAA+TACTCATA	NC_035780.1	2
Processed 26000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2137:15176:14873_1:N:0:AAGTCCAA+TACTCATA	NC_007175.2	17164
Processed 27000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2150:13395:6527_1:N:0:AAGTCCAA+TACTCATA	NC_035780.1	1
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2153:6027:23860_1:N:0:AAGTCCAA+TACTCATA	NC_007175.2	17187
Processed 28000000 sequence pairs so far
Processed 29000000 sequence pairs so far
Processed 30000000 sequence pairs so far
Processed 31000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2249:13991:26349_1:N:0:AAGTCCAA+TACTCATA	NC_007175.2	17183
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2249:8214:26396_1:N:0:AAGTCCAA+TACTCATA	NC_007175.2	17183
Processed 32000000 sequence pairs so far
Processed 33000000 sequence pairs so far
Processed 34000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2334:32515:2002_1:N:0:AAGTCCAA+TACTCATA	NC_007175.2	17199
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2334:31566:3270_1:N:0:AAGTCCAA+TACTCATA	NC_007175.2	17199
Processed 35000000 sequence pairs so far
Processed 36000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2403:28673:10128_1:N:0:AAGTCCAA+TACTCATA	NC_007175.2	17177
Processed 37000000 sequence pairs so far
Processed 38000000 sequence pairs so far
Processed 39000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2444:30427:32863_1:N:0:AAGTCCAA+TACTCATA	NC_007175.2	17199
Processed 40000000 sequence pairs so far
Processed 41000000 sequence pairs so far
Processed 42000000 sequence pairs so far
Processed 43000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2547:31702:9142_1:N:0:AAGTCCAA+TACTCATA	NC_007175.2	17179
Processed 44000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2565:21956:31344_1:N:0:AAGTCCAA+TACTCATA	NC_007175.2	17183
Processed 45000000 sequence pairs so far
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
Processed 52000000 sequence pairs so far
Processed 53000000 sequence pairs so far
Processed 54000000 sequence pairs so far
Processed 55000000 sequence pairs so far
Processed 56000000 sequence pairs so far
Processed 57000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1013:195:GW2105211192nd:2:1237:16523:14575_1:N:0:AAGTCCAA+TACTCATA	NC_007175.2	17161
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
Processed 64000000 sequence pairs so far
Processed 65000000 sequence pairs so far
Processed 66000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1013:195:GW2105211192nd:2:1378:6551:1438_1:N:0:AAGTCCAA+TACTCATA	NC_007175.2	17169
Processed 67000000 sequence pairs so far
Processed 68000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1013:195:GW2105211192nd:2:1422:8748:15984_1:N:0:AAGTCCAA+TACTCATA	NC_007175.2	17135
Processed 69000000 sequence pairs so far
Processed 70000000 sequence pairs so far
Processed 71000000 sequence pairs so far
Processed 72000000 sequence pairs so far
Processed 73000000 sequence pairs so far
Processed 74000000 sequence pairs so far
Processed 75000000 sequence pairs so far
Processed 76000000 sequence pairs so far
Processed 77000000 sequence pairs so far
Processed 78000000 sequence pairs so far
Processed 79000000 sequence pairs so far
Processed 80000000 sequence pairs so far
Processed 81000000 sequence pairs so far
Processed 82000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1013:195:GW2105211192nd:2:1641:14778:19132_1:N:0:AAGTCCAA+TACTCATA	NC_035780.1	2
Processed 83000000 sequence pairs so far
Processed 84000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1013:195:GW2105211192nd:2:1667:25102:32534_1:N:0:AAGTCCAA+TACTCATA	NC_007175.2	2
Processed 85000000 sequence pairs so far
Processed 86000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1013:195:GW2105211192nd:2:2120:8422:12477_1:N:0:AAGTCCAA+TACTCATA	NC_035780.1	2
Chromosomal sequence could not be extracted for	GWNJ-1013:195:GW2105211192nd:2:2120:9588:36761_1:N:0:AAGTCCAA+TACTCATA	NC_035780.1	2
Processed 87000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1013:195:GW2105211192nd:2:2130:4200:26553_1:N:0:AAGTCCAA+TACTCATA	NC_007175.2	17199
Processed 88000000 sequence pairs so far
Processed 89000000 sequence pairs so far
Processed 90000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1013:195:GW2105211192nd:2:2170:13630:26944_1:N:0:AAGTCCAA+TACTCATA	NC_035780.1	1
Processed 91000000 sequence pairs so far
Processed 92000000 sequence pairs so far
Processed 93000000 sequence pairs so far
Processed 94000000 sequence pairs so far
Processed 95000000 sequence pairs so far
Processed 96000000 sequence pairs so far
Processed 97000000 sequence pairs so far
Processed 98000000 sequence pairs so far
Processed 99000000 sequence pairs so far
Processed 100000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1013:195:GW2105211192nd:2:2343:13910:5384_1:N:0:AAGTCCAA+TACTCATA	NC_007175.2	17193
Chromosomal sequence could not be extracted for	GWNJ-1013:195:GW2105211192nd:2:2344:6081:30968_1:N:0:AAGTCCAA+TACTCATA	NC_007175.2	17193
Processed 101000000 sequence pairs so far
Processed 102000000 sequence pairs so far
Processed 103000000 sequence pairs so far
Processed 104000000 sequence pairs so far
Processed 105000000 sequence pairs so far
Processed 106000000 sequence pairs so far
Processed 107000000 sequence pairs so far
Processed 108000000 sequence pairs so far
Processed 109000000 sequence pairs so far
Processed 110000000 sequence pairs so far
Processed 111000000 sequence pairs so far
Processed 112000000 sequence pairs so far
Processed 113000000 sequence pairs so far