Biowulf High Performance Computing at the NIH
roary on Biowulf

Roary is a high speed pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka and calculates the pan genome.

References:

Documentation
Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

For this interactive session we will follow the roary Tutorial. In addition to roary we will also need prokka for annotating the bacterial genomes

[user@biowulf]$ sinteractive --cpus-per-task=6 --mem=20g --gres=lscratch:20
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144]$ module load roary prokka
[user@cn3144]$ cd /lscratch/$SLURM_JOB_ID
[user@cn3144]$ cp $ROARY_TEST_DATA/* .
[user@cn3144]$ ls -1
GCA_000008285.1_ASM828v1_genomic.fna
GCA_000021185.1_ASM2118v1_genomic.fna
GCA_000026705.1_ASM2670v1_genomic.fna
GCA_000168635.2_ASM16863v2_genomic.fna
GCA_000168815.1_ASM16881v1_genomic.fna
GCA_000196035.1_ASM19603v1_genomic.fna

Annotate the genomes with prokka and create a pan genome with roary.

[user@cn3144]$ fastas=( *.fna )
[user@cn3144]$ for fasta in ${fastas[@]}; do
                      acc=${fasta:0:13}
                      prokka --kingdom Bacteria --outdir prokka_$acc --genus Listeria \
                        --locustag $acc --prefix $acc --cpus $SLURM_CPUS_PER_TASK $fasta
                  done

[user@cn3144]$ roary -p $SLURM_CPUS_PER_TASK -f ./roary_demo -e -n -v -r */*.gff
[...snip...]
[user@cn3144]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf]$

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g. roary.sh), which uses the input file 'roary.in'. For example:

#! /bin/bash
# this file is roary.batch

function die {
    echo "$@" >&2
    exit 1
}

wd=$PWD
module load roary/3.12.0 || die "Could not load modules"
cd /lscratch/$SLURM_JOB_ID || die "no lscratch"
roary -p ${SLURM_CPUS_PER_TASK} \
  -f roary_out -e -n -r -v ./gff/*.gff \
&& mv roary_out $wd

Submit this job using the Slurm sbatch command.

sbatch --gres=lscratch:10 --cpus-per-task=6 --mem=6g roary.sh
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

Create a swarmfile (e.g. roary.swarm). For example:

roary -p $SLURM_CPUS_PER_TASK -f ./roary_species1 -e -n -v -r species1/*.gff
roary -p $SLURM_CPUS_PER_TASK -f ./roary_species2 -e -n -v -r species2/*.gff
roary -p $SLURM_CPUS_PER_TASK -f ./roary_species3 -e -n -v -r species3/*.gff

Submit this job using the swarm command.

swarm -f roary.swarm -g 6 -t 6 --module roary/3.12.0
where
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
-t # Number of threads/CPUs required for each process (1 line in the swarm command file).
--module roary Loads the roary module for each subjob in the swarm