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'
Failed to move to ../../data/Mchi/: No such file or directory
USAGE: bismark [options] <genome_folder> {-1 <mates1> -2 <mates2> | <singles>} [<hits>]    (--help for more details)