Purdue University

Commands

• transabyss
• transabyss-merge

Module

You can load the modules by:

module load biocontainers
module load transabyss

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 Transabyss on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 12
#SBATCH --job-name=transabyss
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers transabyss

transabyss --name  SRR12095148 \
    --pe SRR12095148_1.fastq SRR12095148_2.fastq \
    --outdir  SRR12095148_assembly  --threads 12