Purdue University

Commands

• genmap

Module

You can load the modules by:

module load biocontainers
module load genmap

Example job

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run genmap on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=genmap
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers genmap

export TMPDIR=$PWD/tmp
genmap index -F ~/.local/share/genomes/hg38/hg38.fa  -I hg38_index
genmap map -K 64 -E 2 -I hg38_index -O map_output_hg38 -t -w -bg