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 /mmfs1/gscratch/scrubbed/sr320/github/Claudia-Halibut/project/data/genome/	(absolute path is '/mmfs1/gscratch/scrubbed/sr320/github/Claudia-Halibut/project/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/Claudia-Halibut/project/output/02'):
/mmfs1/gscratch/scrubbed/sr320/RRBS-run2/raw-data/E1_T2_C2_R1.fq.gz
/mmfs1/gscratch/scrubbed/sr320/RRBS-run2/raw-data/E1_T2_C2_R2.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/Claudia-Halibut/project/output/02/
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/Claudia-Halibut/project/output/02

Now reading in and storing sequence information of the genome specified in: /mmfs1/gscratch/scrubbed/sr320/github/Claudia-Halibut/project/data/genome/

Single-core mode: setting pid to 1

Paired-end alignments will be performed
=======================================

The provided filenames for paired-end alignments are /mmfs1/gscratch/scrubbed/sr320/RRBS-run2/raw-data/E1_T2_C2_R1.fq.gz and /mmfs1/gscratch/scrubbed/sr320/RRBS-run2/raw-data/E1_T2_C2_R2.fq.gz
Input files are in FastQ format
Writing a C -> T converted version of the input file E1_T2_C2_R1.fq.gz to E1_T2_C2_R1.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file E1_T2_C2_R1.fq.gz to E1_T2_C2_R1.fq.gz_G_to_A.fastq

Created C -> T as well as G -> A converted versions of the FastQ file E1_T2_C2_R1.fq.gz (98619556 sequences in total)

Writing a C -> T converted version of the input file E1_T2_C2_R2.fq.gz to E1_T2_C2_R2.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file E1_T2_C2_R2.fq.gz to E1_T2_C2_R2.fq.gz_G_to_A.fastq

Created C -> T as well as G -> A converted versions of the FastQ file E1_T2_C2_R2.fq.gz (98619556 sequences in total)

Input files are E1_T2_C2_R1.fq.gz_C_to_T.fastq and E1_T2_C2_R1.fq.gz_G_to_A.fastq and E1_T2_C2_R2.fq.gz_C_to_T.fastq and E1_T2_C2_R2.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/Claudia-Halibut/project/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 E1_T2_C2_R1.fq.gz_C_to_T.fastq and E1_T2_C2_R2.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:
lh00134:396:22JL32LT3:2:1101:1703:1064_1:N:0:TCTCTACT+GAACCGCG:AAGTTGTTC/1	77	*	0	0	*	*	0	0	TNATTATAATAATTATTAATATTATATTATTAAATATTTTAATATTTTAATTATTAAGATTGGAAGAGTATATGTTTGAATTTTAGTTATTTTTTATTAAGTTGTTTATTTGGGGGGGGGGGGTGGGGGGTTTTTGGGGGGGGGGGGGGG	I#IIIIIIIIIIIIIIIIII99IIIII9IIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII---I-IIII999I---------------999-99999999-	YT:Z:UP
lh00134:396:22JL32LT3:2:1101:1703:1064_3:N:0:TCTCTACT+GAACCGCG:AAGTTGTTC/2	141	*	0	0	*	*	0	0	TAATAATTAAAATATTAAAATATTTAATAATATAATATTAATAATTATTATAATTAAAATCAAAAAAACATCATATAAAAAAAAAATATAAACCACAATATAAATCTCAATAATTACCATATCATTAAAAAAAAAAAAAAAAAAAAAAAA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-9II-IIII-IIII-I9I-I-IIIIIII-IIIIIIIII-II9-III99I-I-III9-9II9IIIIIIIIIIIII	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from E1_T2_C2_R1.fq.gz_G_to_A.fastq and E1_T2_C2_R2.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:
lh00134:396:22JL32LT3:2:1101:1703:1064_1:N:0:TCTCTACT+GAACCGCG:AAGTTGTTC/1	77	*	0	0	*	*	0	0	CNATTACAATAATCACTAACACCATACCACCAAACACTTCAACACCTTAACCACCAAAATCAAAAAAACACACATCTAAACTCCAATCACTCTCTACTAAATTATTCATCTAAAAAAAAAAAATAAAAAATTTTTAAAAAAAAAAAAAAA	I#IIIIIIIIIIIIIIIIII99IIIII9IIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII---I-IIII999I---------------999-99999999-	YT:Z:UP
lh00134:396:22JL32LT3:2:1101:1703:1064_3:N:0:TCTCTACT+GAACCGCG:AAGTTGTTC/2	141	*	0	0	*	*	0	0	TGGTGGTTAAGGTGTTGAAGTGTTTGGTGGTATGGTGTTAGTGATTATTGTAATTGAGATTGGAAGAGTGTTGTGTAGGGGAAGAGTGTGGATTGTGGTGTAGATTTTGGTGGTTGTTGTATTATTAAAAAAGGGGGGGGGGGGGGGGGG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-9II-IIII-IIII-I9I-I-IIIIIII-IIIIIIIII-II9-III99I-I-III9-9II9IIIIIIIIIIIII	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from E1_T2_C2_R1.fq.gz_G_to_A.fastq and E1_T2_C2_R2.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:
lh00134:396:22JL32LT3:2:1101:1703:1064_1:N:0:TCTCTACT+GAACCGCG:AAGTTGTTC/1	77	*	0	0	*	*	0	0	CNATTACAATAATCACTAACACCATACCACCAAACACTTCAACACCTTAACCACCAAAATCAAAAAAACACACATCTAAACTCCAATCACTCTCTACTAAATTATTCATCTAAAAAAAAAAAATAAAAAATTTTTAAAAAAAAAAAAAAA	I#IIIIIIIIIIIIIIIIII99IIIII9IIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII---I-IIII999I---------------999-99999999-	YT:Z:UP
lh00134:396:22JL32LT3:2:1101:1703:1064_3:N:0:TCTCTACT+GAACCGCG:AAGTTGTTC/2	141	*	0	0	*	*	0	0	TGGTGGTTAAGGTGTTGAAGTGTTTGGTGGTATGGTGTTAGTGATTATTGTAATTGAGATTGGAAGAGTGTTGTGTAGGGGAAGAGTGTGGATTGTGGTGTAGATTTTGGTGGTTGTTGTATTATTAAAAAAGGGGGGGGGGGGGGGGGG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-9II-IIII-IIII-I9I-I-IIIIIII-IIIIIIIII-II9-III99I-I-III9-9II9IIIIIIIIIIIII	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from E1_T2_C2_R1.fq.gz_C_to_T.fastq and E1_T2_C2_R2.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:
lh00134:396:22JL32LT3:2:1101:1703:1064_1:N:0:TCTCTACT+GAACCGCG:AAGTTGTTC/1	77	*	0	0	*	*	0	0	TNATTATAATAATTATTAATATTATATTATTAAATATTTTAATATTTTAATTATTAAGATTGGAAGAGTATATGTTTGAATTTTAGTTATTTTTTATTAAGTTGTTTATTTGGGGGGGGGGGGTGGGGGGTTTTTGGGGGGGGGGGGGGG	I#IIIIIIIIIIIIIIIIII99IIIII9IIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII---I-IIII999I---------------999-99999999-	YT:Z:UP
lh00134:396:22JL32LT3:2:1101:1703:1064_3:N:0:TCTCTACT+GAACCGCG:AAGTTGTTC/2	141	*	0	0	*	*	0	0	TAATAATTAAAATATTAAAATATTTAATAATATAATATTAATAATTATTATAATTAAAATCAAAAAAACATCATATAAAAAAAAAATATAAACCACAATATAAATCTCAATAATTACCATATCATTAAAAAAAAAAAAAAAAAAAAAAAA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-9II-IIII-IIII-I9I-I-IIIIIII-IIIIIIIII-II9-III99I-I-III9-9II9IIIIIIIIIIIII	YT:Z:UP

>>> Writing bisulfite mapping results to E1_T2_C2_pe.bam <<<


Reading in the sequence files /mmfs1/gscratch/scrubbed/sr320/RRBS-run2/raw-data/E1_T2_C2_R1.fq.gz and /mmfs1/gscratch/scrubbed/sr320/RRBS-run2/raw-data/E1_T2_C2_R2.fq.gz
Chromosomal sequence could not be extracted for	lh00134:396:22JL32LT3:2:1101:48488:25866_1:N:0:TCTCTACT+GAACCGCG:GAACCTATG	NW_025899749.1	255680
Chromosomal sequence could not be extracted for	lh00134:396:22JL32LT3:2:1101:48497:25883_1:N:0:TCTCTACT+GAACCGCG:GAACCTATG	NW_025899749.1	255680
Processed 1000000 sequence pairs so far
Chromosomal sequence could not be extracted for	lh00134:396:22JL32LT3:2:1108:36847:2714_1:N:0:TCTCTACT+GAACCGCG:ACATTGGGA	NW_025899749.1	255687
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	lh00134:396:22JL32LT3:2:1124:28036:27757_1:N:0:TCTCTACT+GAACCGCG:ACATTGGGA	NW_025899749.1	255687
Processed 7000000 sequence pairs so far
Chromosomal sequence could not be extracted for	lh00134:396:22JL32LT3:2:1129:21942:24953_1:N:0:TCTCTACT+GAACCGCG:GTTAGGGGT	NW_025899749.1	255683
Processed 8000000 sequence pairs so far
Processed 9000000 sequence pairs so far
Processed 10000000 sequence pairs so far
Processed 11000000 sequence pairs so far
(ERR): bowtie2-align exited with value 141
(ERR): bowtie2-align exited with value 141
(ERR): bowtie2-align exited with value 141
(ERR): bowtie2-align exited with value 141