Hello,

I am trying to map bisulfite sequencing data files with the help of Bismark. I am getting an error while running this tool on command line. could you help with this issue? Thanks in advance.

 $ bismark --bowtie2 -n 1 -l 50  /scratch/user/mayurdoke/Genome2/control1.fasta

Bowtie 2 seems to be working fine (tested command bowtie2 --version [2.3.5])

Output format is BAM (default)

Alignments will be written out in BAM format. Samtools found here: /sw/eb/software/SAMtools/1.9-intel-2018b/bin/samtools

Failed to move to /scratch/user/mayurdoke/Genome2/control1.fasta/: No such file or directory
USAGE: bismark [options] <genome_folder> {-1 <mates1> -2 <mates2> | <singles>} [<hits>]    (--help for more details)