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/EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz
../../data/EF01-EM01-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/EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz and ../../data/EF01-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz
Input files are in FastQ format
Writing a C -> T converted version of the input file EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz to EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz to EF01-EM01-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 EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz (123554588 sequences in total)

Writing a C -> T converted version of the input file EF01-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz to EF01-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file EF01-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz to EF01-EM01-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 EF01-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz (123554588 sequences in total)

Input files are EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz_C_to_T.fastq and EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz_G_to_A.fastq and EF01-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz_C_to_T.fastq and EF01-EM01-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 EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz_C_to_T.fastq and EF01-EM01-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:GW210315000:4:1101:27353:1047_1:N:0:TAATACAG+GTGAATAT/1	77	*	0	0	*	*	0	0	ANTAATATTTTTTTTTTAATAATTATTTTTTTTTTTTTATAATTAATATATAATATATTTTTTTTTTTTTATTTTTAATAATATTAGAA	F#FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	YT:Z:UP
GWNJ-1012:512:GW210315000:4:1101:27353:1047_2:N:0:TAATACAG+GTGAATAT/2	141	*	0	0	*	*	0	0	TTCTAATATTATTAAAAATAAAAAAAAAAAAATATATTATATATTAATTATAAAAAAAAAAAAATAATTATTAAAAAAAAAATATTAAT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz_G_to_A.fastq and EF01-EM01-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:GW210315000:4:1101:27353:1047_1:N:0:TAATACAG+GTGAATAT/1	99	NC_035787.1_GA_converted	25129866	0	57M1I31M	=	25129866	88	ANCAACACTTTTTCTTTAATAATCATTTTTTTCTTTTTATAACTAACATATAATATACTTTTTTCCTCTTATTTCTAACAACATTAAAA	F#FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	AS:i:-69	XS:i:-69	XN:i:0	XM:i:11	XO:i:1	XG:i:1	NM:i:12	MD:Z:1T3T11T1C1T2T32A4A22T0T0T0	YS:i:-68	YT:Z:CP
GWNJ-1012:512:GW210315000:4:1101:27353:1047_2:N:0:TAATACAG+GTGAATAT/2	147	NC_035787.1_GA_converted	25129866	0	57M1I31M	=	25129866	-88	ATCAACACTTTTTCTTTAATAATCATTTTTTTCTTTTTATAACTAACATATAATATACTTTTTTCCTCTTATTTCTAACAACATTAAAA	FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	AS:i:-68	XS:i:-68	XN:i:0	XM:i:10	XO:i:1	XG:i:1	NM:i:11	MD:Z:5T11T1C1T2T32A4A22T0T0T0	YS:i:-69	YT:Z:CP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz_G_to_A.fastq and EF01-EM01-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:GW210315000:4:1101:27353:1047_1:N:0:TAATACAG+GTGAATAT/1	83	NC_035785.1_CT_converted	2145616	0	25M1I63M	=	2145616	-88	TTTTAATGTTGTTAGAAATAAGAGGAAAAAAGTATATTATATGTTAGTTATAAAAAGAAAAAAATGATTATTAAAGAAAAAGTGTTGNT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF#F	AS:i:-69	XS:i:-69	XN:i:0	XM:i:11	XO:i:1	XG:i:1	NM:i:12	MD:Z:0A0A0A22T4T32A2A1G1G11A3A1	YS:i:-68	YT:Z:CP
GWNJ-1012:512:GW210315000:4:1101:27353:1047_2:N:0:TAATACAG+GTGAATAT/2	163	NC_035785.1_CT_converted	2145616	0	25M1I63M	=	2145616	88	TTTTAATGTTGTTAGAAATAAGAGGAAAAAAGTATATTATATGTTAGTTATAAAAAGAAAAAAATGATTATTAAAGAAAAAGTGTTGAT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF	AS:i:-68	XS:i:-68	XN:i:0	XM:i:10	XO:i:1	XG:i:1	NM:i:11	MD:Z:0A0A0A22T4T32A2A1G1G11A5	YS:i:-69	YT:Z:CP
Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz_C_to_T.fastq and EF01-EM01-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:GW210315000:4:1101:27353:1047_1:N:0:TAATACAG+GTGAATAT/1	77	*	0	0	*	*	0	0	ANTAATATTTTTTTTTTAATAATTATTTTTTTTTTTTTATAATTAATATATAATATATTTTTTTTTTTTTATTTTTAATAATATTAGAA	F#FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	YT:Z:UP
GWNJ-1012:512:GW210315000:4:1101:27353:1047_2:N:0:TAATACAG+GTGAATAT/2	141	*	0	0	*	*	0	0	TTCTAATATTATTAAAAATAAAAAAAAAAAAATATATTATATATTAATTATAAAAAAAAAAAAATAATTATTAAAAAAAAAATATTAAT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF	YT:Z:UP

>>> Writing bisulfite mapping results to EF01-EM01-Zygote_pe.bam <<<


Reading in the sequence files ../../data/EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz and ../../data/EF01-EM01-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
Processed 5000000 sequence pairs so far
Processed 6000000 sequence pairs so far
Processed 7000000 sequence pairs so far
Processed 8000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:1305:16459:27962_1:N:0:TAATACAG+ATGAATAT	NC_007175.2	1
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:1305:15555:28494_1:N:0:TAATACAG+ATGAATAT	NC_007175.2	1
Processed 9000000 sequence pairs so far
Processed 10000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:1335:15383:33395_1:N:0:TAATACAG+GTGAATAT	NC_007175.2	2
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:1339:6117:22639_1:N:0:TAATACAG+GTGAATAT	NC_007175.2	2
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:GW210315000:4:1429:2383:27289_1:N:0:TAATACAG+GTGAATAT	NC_007175.2	2
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:1430:25382:30420_1:N:0:TAATACAG+GTGAATAT	NC_035780.1	3
Processed 14000000 sequence pairs so far
Processed 15000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:1473:19533:21198_1:N:0:TAATACAG+GTGAATAT	NC_007175.2	17153
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:1473:18295:22874_1:N:0:TAATACAG+GTGAATAT	NC_007175.2	17153
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:1473:19108:23657_1:N:0:TAATACAG+GTGAATAT	NC_007175.2	17153
Processed 16000000 sequence pairs so far
Processed 17000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:1515:30535:19805_1:N:0:TAATACAG+GTGAATAT	NC_007175.2	2
Processed 18000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:1540:11749:5212_1:N:0:TAATACAG+GTGAATAT	NC_007175.2	2
Processed 19000000 sequence pairs so far
Processed 20000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:1601:28447:2691_1:N:0:TAATACAG+GTGAATAT	NC_007175.2	2
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:GW210315000:4:2119:16324:35180_1:N:0:TAATACAG+GTGAATAT	NC_035780.1	2
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2131:25997:35963_1:N:0:TAATACAG+GTGAATAT	NC_007175.2	1
Processed 26000000 sequence pairs so far
Processed 27000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2169:10963:6543_1:N:0:TAATACAG+GTGAATAT	NC_007175.2	2
Processed 28000000 sequence pairs so far
Processed 29000000 sequence pairs so far
Processed 30000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2252:3170:20071_1:N:0:TAATACAG+GTGAATAT	NC_007175.2	2
Processed 31000000 sequence pairs so far
Processed 32000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2274:27082:12571_1:N:0:TAATACAG+GTGAATAT	NC_007175.2	2
Processed 33000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2318:15266:18443_1:N:0:TAATACAG+GTGAATAT	NC_007175.2	2
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2332:8567:4993_1:N:0:TAATACAG+GGGAATAT	NC_007175.2	2
Processed 34000000 sequence pairs so far
Processed 35000000 sequence pairs so far
Processed 36000000 sequence pairs so far
Processed 37000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2431:21287:3630_1:N:0:TAATACAG+GTGAATAT	NC_035780.1	3
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2431:21513:3709_1:N:0:TAATACAG+GTGAATAT	NC_035780.1	3
Processed 38000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2444:3396:19116_1:N:0:TAATACAG+GTGAATAT	NC_007175.2	2
Processed 39000000 sequence pairs so far
Processed 40000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2474:15275:13573_1:N:0:TAATACAG+GTGAATAT	NC_007175.2	17153
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2510:1714:17519_1:N:0:TAATACAG+GTGAATAT	NC_035781.1	2
Processed 41000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2521:12753:28588_1:N:0:TAATACAG+GTGAATAT	NC_007175.2	2
Processed 42000000 sequence pairs so far
Processed 43000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2571:15908:32863_1:N:0:TAATACAG+GTGTATAT	NC_007175.2	2
Processed 44000000 sequence pairs so far
Processed 45000000 sequence pairs so far
Processed 46000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2642:17942:3223_1:N:0:TAATACAG+GTGAATAT	NC_007175.2	2
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2642:17065:4335_1:N:0:TAATACAG+GTGAATAT	NC_007175.2	2
Processed 47000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2668:27724:8328_1:N:0:TAATACAG+GTGAATAT	NC_007175.2	2
Processed 48000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2678:17707:2002_1:N:0:TAATACAG+GTGAATAT	NC_035781.1	2
Chromosomal sequence could not be extracted for	GWNJ-1013:195:GW2105211192nd:2:1107:22616:31641_1:N:0:TAATACAG+GTGAATAT	NC_035780.1	1
Processed 49000000 sequence pairs so far
Processed 50000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1013:195:GW2105211192nd:2:1127:25021:12602_1:N:0:TAATACAG+GTGAATAT	NC_007175.2	1
Processed 51000000 sequence pairs so far
Processed 52000000 sequence pairs so far
Processed 53000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1013:195:GW2105211192nd:2:1161:31213:1689_1:N:0:TAATACAG+GTGAATAT	NC_007175.2	2
Chromosomal sequence could not be extracted for	GWNJ-1013:195:GW2105211192nd:2:1171:16260:25175_1:N:0:TAATACAG+GTGAATAT	NC_007175.2	1
Chromosomal sequence could not be extracted for	GWNJ-1013:195:GW2105211192nd:2:1171:14326:25801_1:N:0:TAATACAG+GTGAATAT	NC_007175.2	1
Processed 54000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1013:195:GW2105211192nd:2:1175:32127:26036_1:N:0:TAATACAG+GTGAATAT	NC_035781.1	2
Chromosomal sequence could not be extracted for	GWNJ-1013:195:GW2105211192nd:2:1202:22083:16282_1:N:0:TAATACAG+GTGAATAT	NC_035780.1	2
Chromosomal sequence could not be extracted for	GWNJ-1013:195:GW2105211192nd:2:1202:22643:19601_1:N:0:TAATACAG+GTGAATAT	NC_035780.1	2
Processed 55000000 sequence pairs so far
Processed 56000000 sequence pairs so far
Processed 57000000 sequence pairs so far
Processed 58000000 sequence pairs so far
Processed 59000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1013:195:GW2105211192nd:2:1258:13874:16939_1:N:0:TAATACAG+GTGAATAT	NC_007175.2	2
Processed 60000000 sequence pairs so far
Processed 61000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1013:195:GW2105211192nd:2:1314:3911:32127_1:N:0:TAATACAG+GTGAATAT	NC_007175.2	2
Processed 62000000 sequence pairs so far
Processed 63000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1013:195:GW2105211192nd:2:1339:17119:10347_1:N:0:TAATACAG+GTGAATAT	NC_007175.2	17157
Processed 64000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1013:195:GW2105211192nd:2:1342:30156:37027_1:N:0:TAATACAG+GTGAATAT	NC_007175.2	2
Chromosomal sequence could not be extracted for	GWNJ-1013:195:GW2105211192nd:2:1343:30626:1172_1:N:0:TAATACAG+GTGAATAT	NC_007175.2	2
Processed 65000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1013:195:GW2105211192nd:2:1355:12572:16752_1:N:0:TAATACAG+GTGAATAT	NC_007175.2	1
Chromosomal sequence could not be extracted for	GWNJ-1013:195:GW2105211192nd:2:1361:22381:21089_1:N:0:TAATACAG+GTGAATAT	NC_007175.2	17160
Processed 66000000 sequence pairs so far
Processed 67000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1013:195:GW2105211192nd:2:1407:27118:22435_1:N:0:TAATACAG+GTGAATAT	NC_007175.2	2
Chromosomal sequence could not be extracted for	GWNJ-1013:195:GW2105211192nd:2:1407:29080:26334_1:N:0:TAATACAG+GGGAATAT	NC_007175.2	2
Processed 68000000 sequence pairs so far