We have customised VirSorter slightly for the cluster environment:

  • The number of jobs must be specified
  • We default to --skip-deps-installand --use-conda-off

We don't provide the VirSorter databases, so you will have to run virsorter setup first

If you are doing many runs, it is good practice to use the --rm-tmpdir option to delete all the temporary files which VirSorter makes, and so reduce the risk of reaching your file quota.

VirSorter defaults its LOCAL_SCRATCH configuration setting to "/tmp", but we would prefer that Slurm jobs instead use the automatically cleaned up per-job directory $TMPDIR. This is actually a Snakemake rule configuration, so can be set at the end of the virsorter command line.

So an example which uses the SLURM_CPUS_PER_TASK and TMPDIR values provided to Slurm jobs would be:

module load VirSorter/2.1-gimkl-2020a-Python-3.8.2
virsorter run \
--seqfile test.fasta \
--jobs ${SLURM_CPUS_PER_TASK:-2} \
--rm-tmpdir \
all \
--config LOCAL_SCRATCH=${TMPDIR:-/tmp}


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