Purdue University

Commands

• quiver
• arrow
• variantCaller

Module

You can load the modules by:

module load biocontainers
module load genomicconsensus

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 Genomicconsensus on our clusters:

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

module --force purge
ml biocontainers genomicconsensus

quiver -j12 out.aligned_subreads.bam \ 
    -r All4mer.V2.01_Insert-changed.fa  \
    -o consensus.fasta -o consensus.fastq