Path to genome folder specified as: /gscratch/srlab/sr320/data/froger/Mcap_Genome_02/
Using 28 threads for the top and bottom strand indexing processes each, so using 56 cores in total
Aligner to be used: >> Bowtie 2 << (default)
Writing bisulfite genomes out into a single MFA (multi FastA) file

Bismark Genome Preparation - Step I: Preparing folders

Path to Bowtie 2 specified as: /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/
The specified genome folder /gscratch/srlab/sr320/data/froger/Mcap_Genome_02/ does not contain any sequence files in FastA format (with .fa, .fa.gz, .fasta or .fasta.gz file extensions)