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_T1_C2_R1.fq.gz
/mmfs1/gscratch/scrubbed/sr320/RRBS-run2/raw-data/E1_T1_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_T1_C2_R1.fq.gz and /mmfs1/gscratch/scrubbed/sr320/RRBS-run2/raw-data/E1_T1_C2_R2.fq.gz
Input files are in FastQ format
Writing a C -> T converted version of the input file E1_T1_C2_R1.fq.gz to E1_T1_C2_R1.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file E1_T1_C2_R1.fq.gz to E1_T1_C2_R1.fq.gz_G_to_A.fastq

Created C -> T as well as G -> A converted versions of the FastQ file E1_T1_C2_R1.fq.gz (104370060 sequences in total)

Writing a C -> T converted version of the input file E1_T1_C2_R2.fq.gz to E1_T1_C2_R2.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file E1_T1_C2_R2.fq.gz to E1_T1_C2_R2.fq.gz_G_to_A.fastq

Created C -> T as well as G -> A converted versions of the FastQ file E1_T1_C2_R2.fq.gz (104370060 sequences in total)

Input files are E1_T1_C2_R1.fq.gz_C_to_T.fastq and E1_T1_C2_R1.fq.gz_G_to_A.fastq and E1_T1_C2_R2.fq.gz_C_to_T.fastq and E1_T1_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_T1_C2_R1.fq.gz_C_to_T.fastq and E1_T1_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:
lh00134:396:22JL32LT3:2:1101:1148:1064_1:N:0:AGTTCAGG+TCTGTTGG:ACACACGAG/1	77	*	0	0	*	*	0	0	TNAATTTAAATTTTATTATAAATTTAAAATTTTTATGTAATTTGAAATTTAAATTATATTTATATTAATTTTAAAATTAATTAATTTTTGATATTATTTTTAAATTTATAATTAATAAAATTTTAAAAATTGAGATTGGAAGATTATTTT	9#IIIIIII-III9IIIIIIIIIIIII9IIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII9II9IIIIII9IIII99I9-IIII-III-I-	YT:Z:UP
lh00134:396:22JL32LT3:2:1101:1148:1064_3:N:0:AGTTCAGG+TCTGTTGG:ACACACGAG/2	141	*	0	0	*	*	0	0	CAATTTTTAAAATTTTATTAATTATAAATTTAAAAATAATATCAAAAATTAATTAATTTTAAAATTAATATAAATATAATTTAAATTTCAAATTACATAAAAATTTTAAATTTATAATAAAATTTAAATTTAAAATCAAAAAAACATCAT	II9I9IIII9IIIIIII9IIII9IIIIIIIIII9IIIIIIIIIIII9I-IIIII-IIIIIII9IIIIII9IIIIIII9IIIIIIII-IIIIII9IIIIIIIII9IIIIIIIII9IIIIIIII9III9IIIIIIIIIII-IIIIIIIIIII	YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from E1_T1_C2_R1.fq.gz_G_to_A.fastq and E1_T1_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:
lh00134:396:22JL32LT3:2:1101:1148:1064_1:N:0:AGTTCAGG+TCTGTTGG:ACACACGAG/1	99	NC_061503.1_GA_converted	108825	2	136M4I10M	=	108812	-159	CNAACTTAAACTCTACTACAAATCTAAAACCCCTACATAATTCAAAACCCAAACTACACCTATATTAATTTCAAAATCAACTAACCTCTAACATCATCTTTAAACCTATAACTAACAAAACTTTAAAAACCAAAATCAAAAAATCACTCT	9#IIIIIII-III9IIIIIIIIIIIII9IIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII9II9IIIIII9IIII99I9-IIII-III-I-	AS:i:-54	XS:i:-54	XN:i:0	XM:i:7	XO:i:1	XG:i:4	NM:i:11	MD:Z:1A63A68C4C3C0A0A0	YS:i:-54	YT:Z:CP
lh00134:396:22JL32LT3:2:1101:1148:1064_3:N:0:AGTTCAGG+TCTGTTGG:ACACACGAG/2	147	NC_061503.1_GA_converted	108812	2	5M3I1M1I7M1I132M	=	108825	159	ACAACACTCTTCCAATCTCAAACTTAAACTCTACTACAAATCTAAAACCCCTACATAATTCAAAACCCAAACTACACCTATATTAATTTCAAAATCAACTAACCTCTAACATCATCTTTAAACCTATAACTAACAAAACTTTAAAAACCA	IIIIIIIIIII-IIIIIIIIIII9III9IIIIIIII9IIIIIIIII9IIIIIIIII9IIIIII-IIIIIIII9IIIIIII9IIIIII9IIIIIII-IIIII-I9IIIIIIIIIIII9IIIIIIIIII9IIII9IIIIIII9IIII9I9II	AS:i:-54	XS:i:-55	XN:i:0	XM:i:4	XO:i:3	XG:i:5	NM:i:9	MD:Z:7A0A2A66A66	YS:i:-54	YT:Z:CP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from E1_T1_C2_R1.fq.gz_G_to_A.fastq and E1_T1_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:
lh00134:396:22JL32LT3:2:1101:1148:1064_1:N:0:AGTTCAGG+TCTGTTGG:ACACACGAG/1	83	NC_061505.1_CT_converted	16606866	0	10M4I136M	=	16606880	161	AGAGTGATTTTTTGATTTTGGTTTTTAAAGTTTTGTTAGTTATAGGTTTAAAGATGATGTTAGAGGTTAGTTGATTTTGAAATTAATATAGGTGTAGTTTGGGTTTTGAATTATGTAGGGGTTTTAGATTTGTAGTAGAGTTTAAGTTNG	-I-III-IIII-9I99IIII9IIIIII9II9IIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIII9IIIIIIIIIIIII9III-IIIIIII#9	AS:i:-54	XN:i:0	XM:i:7	XO:i:1	XG:i:4	NM:i:11	MD:Z:0T0T0G3G4G68T63T1	YS:i:-55	YT:Z:CP
lh00134:396:22JL32LT3:2:1101:1148:1064_3:N:0:AGTTCAGG+TCTGTTGG:ACACACGAG/2	163	NC_061505.1_CT_converted	16606880	0	137M2I3M1I7M	=	16606866	-161	TGGTTTTTAAAGTTTTGTTAGTTATAGGTTTAAAGATGATGTTAGAGGTTAGTTGATTTTGAAATTAATATAGGTGTAGTTTGGGTTTTGAATTATGTAGGGGTTTTAGATTTGTAGTAGAGTTTAAGTTTGAGATTGGAAGAGTGTTGT	II9I9IIII9IIIIIII9IIII9IIIIIIIIII9IIIIIIIIIIII9I-IIIII-IIIIIII9IIIIII9IIIIIII9IIIIIIII-IIIIII9IIIIIIIII9IIIIIIIII9IIIIIIII9III9IIIIIIIIIII-IIIIIIIIIII	AS:i:-55	XS:i:-85	XN:i:0	XM:i:6	XO:i:2	XG:i:3	NM:i:9	MD:Z:66T65G0T3T3A1G3	YS:i:-54	YT:Z:CP
Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from E1_T1_C2_R1.fq.gz_C_to_T.fastq and E1_T1_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:
lh00134:396:22JL32LT3:2:1101:1148:1064_1:N:0:AGTTCAGG+TCTGTTGG:ACACACGAG/1	77	*	0	0	*	*	0	0	TNAATTTAAATTTTATTATAAATTTAAAATTTTTATGTAATTTGAAATTTAAATTATATTTATATTAATTTTAAAATTAATTAATTTTTGATATTATTTTTAAATTTATAATTAATAAAATTTTAAAAATTGAGATTGGAAGATTATTTT	9#IIIIIII-III9IIIIIIIIIIIII9IIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII9II9IIIIII9IIII99I9-IIII-III-I-	YT:Z:UP
lh00134:396:22JL32LT3:2:1101:1148:1064_3:N:0:AGTTCAGG+TCTGTTGG:ACACACGAG/2	141	*	0	0	*	*	0	0	CAATTTTTAAAATTTTATTAATTATAAATTTAAAAATAATATCAAAAATTAATTAATTTTAAAATTAATATAAATATAATTTAAATTTCAAATTACATAAAAATTTTAAATTTATAATAAAATTTAAATTTAAAATCAAAAAAACATCAT	II9I9IIII9IIIIIII9IIII9IIIIIIIIII9IIIIIIIIIIII9I-IIIII-IIIIIII9IIIIII9IIIIIII9IIIIIIII-IIIIII9IIIIIIIII9IIIIIIIII9IIIIIIII9III9IIIIIIIIIII-IIIIIIIIIII	YT:Z:UP

>>> Writing bisulfite mapping results to E1_T1_C2_pe.bam <<<


Reading in the sequence files /mmfs1/gscratch/scrubbed/sr320/RRBS-run2/raw-data/E1_T1_C2_R1.fq.gz and /mmfs1/gscratch/scrubbed/sr320/RRBS-run2/raw-data/E1_T1_C2_R2.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
(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