Bowtie 2 seems to be working fine (tested command '/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2 --version' [2.4.4])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools found here: '/usr/bin/samtools'
Reference genome folder provided is ../data/genome/	(absolute path is '/home/shared/8TB_HDD_03/sr320/github/ceasmallr/data/genome/)'
FastQ format assumed (by default)
Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary!

Input files to be analysed (in current folder '/home/shared/8TB_HDD_03/sr320/github/ceasmallr/code'):
../data/EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz
../data/EF07-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: /home/shared/8TB_HDD_03/sr320/github/ceasmallr/output/01-data-explore/bismark/
Setting parallelization to single-threaded (default)

Summary of all aligner options:	-q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500
Current working directory is: /home/shared/8TB_HDD_03/sr320/github/ceasmallr/code

Now reading in and storing sequence information of the genome specified in: /home/shared/8TB_HDD_03/sr320/github/ceasmallr/data/genome/

chr NC_035780.1 (65668440 bp)
chr NC_035781.1 (61752955 bp)
chr NC_035782.1 (77061148 bp)
chr NC_035783.1 (59691872 bp)
chr NC_035784.1 (98698416 bp)
chr NC_035785.1 (51258098 bp)
chr NC_035786.1 (57830854 bp)
chr NC_035787.1 (75944018 bp)
chr NC_035788.1 (104168038 bp)
chr NC_035789.1 (32650045 bp)
chr NC_007175.2 (17244 bp)

Single-core mode: setting pid to 1

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

The provided filenames for paired-end alignments are ../data/EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz and ../data/EF07-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 EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz to EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz to EF07-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 EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz (241349617 sequences in total)

Writing a C -> T converted version of the input file EF07-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz to EF07-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file EF07-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz to EF07-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz_G_to_A.fastq

gzip: ../data/EF07-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz: unexpected end of file

Created C -> T as well as G -> A converted versions of the FastQ file EF07-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz (29076567 sequences in total)

[FATAL ERROR]:	Number of bisulfite transformed reads are not equal between Read 1 (#241349617) and Read 2 (#29076567).
Possible causes: file truncation, or as a result of specifying read pairs that do not belong to each other?! Please re-specify file names! Exiting...

xargs: /home/shared/Bismark-0.24.0/bismark: exited with status 255; aborting