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/EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz
../../data/EF08-EM03-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/EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz and ../../data/EF08-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz
Input files are in FastQ format
Writing a C -> T converted version of the input file EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz to EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz to EF08-EM03-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 EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz (163523227 sequences in total)

Writing a C -> T converted version of the input file EF08-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz to EF08-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file EF08-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz to EF08-EM03-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 EF08-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz (163523227 sequences in total)

Input files are EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz_C_to_T.fastq and EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz_G_to_A.fastq and EF08-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz_C_to_T.fastq and EF08-EM03-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 EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz_C_to_T.fastq and EF08-EM03-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:GW210315000:4:1101:25400:1047_1:N:0:AATGCCTC+TGGATCGA/1	77	*	0	0	*	*	0	0	TNATAAATTAATTAAATTTTTATTAATTTTTAAATTTTTTAAAATTTTTATTTTATATAATAATAAATTTTTTTTAATAATAATAAATTATATTATTAAATAAATAAATATATTTTTTTATTATTTTTAAATAATTAAAATTATTTT	F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	YT:Z:UP
GWNJ-1012:512:GW210315000:4:1101:25400:1047_2:N:0:AATGCCTC+TGGATCGA/2	141	*	0	0	*	*	0	0	AAAATAATTTTAATTATTTAAAAATAATAAAAAAATATATTTATTTATTTAATAATATAATTTATTATTATTAAAAAAAATTTATTATTATATAAAATAAAAATTTTAAAAAATTTAAAAATTAATAAAAATTTAATTAATTTATTA	FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFF:F:FFFFFFFFFFFFFFFFFFFF:FFFFFF	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz_G_to_A.fastq and EF08-EM03-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:GW210315000:4:1101:25400:1047_1:N:0:AATGCCTC+TGGATCGA/1	99	NC_035787.1_GA_converted	40960853	3	105M1D17M1I24M	=	40960853	147	CNACAAATCAACTAAACCTTTACTAATCTCTAAATTTTCTAAAACTCTTACCCCATACAATAATAAATTTTTCCTAATAATAATAAACCATATCACCAAATAAATAAATACATCCCCTTACCATTCCTAAACAACTAAAATTACCCC	F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	AS:i:-71	XN:i:0	XM:i:10	XO:i:2	XG:i:2	NM:i:12	MD:Z:1T0C42C23C0A19A0T13^A17C3C17A1	YS:i:-76	YT:Z:CP
GWNJ-1012:512:GW210315000:4:1101:25400:1047_2:N:0:AATGCCTC+TGGATCGA/2	147	NC_035787.1_GA_converted	40960853	3	105M1D17M1I24M	=	40960853	-147	CAACAAATCAACTAAACCTTTACTAATCTCTAAATTTTCTAAAACTCTTACCCCATACAATAATAAATTTTTCCTAATAATAATAAACCATATCACCAAATAAATAAATACATCCCCTTACCATTCCTAAACAACTAAAATTACCCC	FFFFFF:FFFFFFFFFFFFFFFFFFFF:F:FFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF,FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF	AS:i:-76	XN:i:0	XM:i:10	XO:i:2	XG:i:2	NM:i:12	MD:Z:1T0C42C23C0A19A0T13^A17C3C17A1	YS:i:-71	YT:Z:CP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz_G_to_A.fastq and EF08-EM03-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:GW210315000:4:1101:25400:1047_1:N:0:AATGCCTC+TGGATCGA/1	83	NC_035787.1_CT_converted	43773939	2	19M1I19M1D108M	=	43773939	-147	GGGGTAATTTTAGTTGTTTAGGAATGGTAAGGGGATGTATTTATTTATTTGGTGATATGGTTTATTATTATTAGGAAAAATTTATTATTGTATGGGGTAAGAGTTTTAGAAAATTTAGAGATTAGTAAAGGTTTAGTTGATTTGTNG	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#F	AS:i:-95	XS:i:-101	XN:i:0	XM:i:14	XO:i:2	XG:i:2	NM:i:16	MD:Z:1T19G1G5T8^T6G7A1A0T6T12T0G11T11G43A1	YS:i:-100	YT:Z:CP
GWNJ-1012:512:GW210315000:4:1101:25400:1047_2:N:0:AATGCCTC+TGGATCGA/2	163	NC_035787.1_CT_converted	43773939	2	19M1I19M1D108M	=	43773939	147	GGGGTAATTTTAGTTGTTTAGGAATGGTAAGGGGATGTATTTATTTATTTGGTGATATGGTTTATTATTATTAGGAAAAATTTATTATTGTATGGGGTAAGAGTTTTAGAAAATTTAGAGATTAGTAAAGGTTTAGTTGATTTGTTG	FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFF:F:FFFFFFFFFFFFFFFFFFFF:FFFFFF	AS:i:-100	XS:i:-106	XN:i:0	XM:i:14	XO:i:2	XG:i:2	NM:i:16	MD:Z:1T19G1G5T8^T6G7A1A0T6T12T0G11T11G43A1	YS:i:-95	YT:Z:CP
Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz_C_to_T.fastq and EF08-EM03-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:GW210315000:4:1101:25400:1047_1:N:0:AATGCCTC+TGGATCGA/1	77	*	0	0	*	*	0	0	TNATAAATTAATTAAATTTTTATTAATTTTTAAATTTTTTAAAATTTTTATTTTATATAATAATAAATTTTTTTTAATAATAATAAATTATATTATTAAATAAATAAATATATTTTTTTATTATTTTTAAATAATTAAAATTATTTT	F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	YT:Z:UP
GWNJ-1012:512:GW210315000:4:1101:25400:1047_2:N:0:AATGCCTC+TGGATCGA/2	141	*	0	0	*	*	0	0	AAAATAATTTTAATTATTTAAAAATAATAAAAAAATATATTTATTTATTTAATAATATAATTTATTATTATTAAAAAAAATTTATTATTATATAAAATAAAAATTTTAAAAAATTTAAAAATTAATAAAAATTTAATTAATTTATTA	FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFF:F:FFFFFFFFFFFFFFFFFFFF:FFFFFF	YT:Z:UP

>>> Writing bisulfite mapping results to EF08-EM03-Larvae_pe.bam <<<


Reading in the sequence files ../../data/EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz and ../../data/EF08-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:1114:18837:28416_1:N:0:AATGCCTC+TGGATCGA	NC_035780.1	3
Processed 1000000 sequence pairs so far
Processed 2000000 sequence pairs so far
Processed 3000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:1171:28420:16016_1:N:0:AATGCCTC+TGGATCGA	NC_035780.1	2
Processed 4000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:1174:4200:10802_1:N:0:AATGCCTC+TGGATCGA	NC_035781.1	3
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
Processed 11000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:1359:25301:2910_1:N:0:AATGCCTC+TGGATCGA	NC_035780.1	1
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
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:1464:26793:18208_1:N:0:AATGCCTC+TGGATCGA	NC_035780.1	3
Processed 17000000 sequence pairs so far
Processed 18000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:1524:8232:1407_1:N:0:AATGCCTC+TGGATCGA	NC_035780.1	2
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
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:1662:3812:11913_1:N:0:AATGCCTC+TGGATCGA	NC_035780.1	2
Processed 25000000 sequence pairs so far
Processed 26000000 sequence pairs so far
Processed 27000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2137:8196:24862_1:N:0:AATGCCTC+TGGATCGA	NC_035780.1	2
Processed 28000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2148:17580:20854_1:N:0:AATGCCTC+TGGATCGA	NC_035780.1	2
Processed 29000000 sequence pairs so far
Processed 30000000 sequence pairs so far
Processed 31000000 sequence pairs so far
Processed 32000000 sequence pairs so far
Processed 33000000 sequence pairs so far
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:GW210315000:4:2367:2049:25081_1:N:0:AATGCCTC+TGGATCGA	NC_035780.1	2
Processed 38000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2401:30056:31313_1:N:0:AATGCCTC+TGGATCGA	NC_035780.1	2
Processed 39000000 sequence pairs so far
Processed 40000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2434:2826:3223_1:N:0:AATGCCTC+TGGATCGA	NC_035781.1	2
Processed 41000000 sequence pairs so far
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
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2602:29170:28181_1:N:0:AATGCCTC+TGGATCGA	NC_035780.1	2
Processed 47000000 sequence pairs so far
Processed 48000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2628:31584:13510_1:N:0:AATGCCTC+TGGATCGA	NC_035781.1	2
Processed 49000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2652:3893:17722_1:N:0:AATGCCTC+TGGATCGA	NC_035780.1	2
Chromosomal sequence could not be extracted for	GWNJ-1012:512:GW210315000:4:2652:3812:17832_1:N:0:AATGCCTC+TGGATCGA	NC_035780.1	2
Processed 50000000 sequence pairs so far
Processed 51000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1013:195:GW2105211192nd:2:1105:24144:15499_1:N:0:AATGCCTC+TGGATCGA	NC_035780.1	2
Processed 52000000 sequence pairs so far
Processed 53000000 sequence pairs so far
Processed 54000000 sequence pairs so far
Processed 55000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1013:195:GW2105211192nd:2:1137:5999:14387_1:N:0:AATGCCTC+TGGATCGA	NC_035780.1	3
Chromosomal sequence could not be extracted for	GWNJ-1013:195:GW2105211192nd:2:1137:6470:18677_1:N:0:AATGCCTC+TGGATCGA	NC_035780.1	3
Processed 56000000 sequence pairs so far
Chromosomal sequence could not be extracted for	GWNJ-1013:195:GW2105211192nd:2:1149:10041:5102_1:N:0:AATGCCTC+TGGATCGA	NC_035780.1	2
Chromosomal sequence could not be extracted for	GWNJ-1013:195:GW2105211192nd:2:1150:10755:32800_1:N:0:AATGCCTC+TGGATCGA	NC_035780.1	2