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)
Processing sequences up to read no. 10000 from the input file
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/04-bismark-align'):
Supplied filename '../../data/CF08-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz_R1_001.fastp-trim.20220827.fq.gz' does not exist, please respecify!