QUAST on Biowulf

QUAST stands for QUality ASsessment Tool. The tool evaluates genome assemblies by computing various metrics. The package includes the general QUAST tool for genome assemblies, MetaQUAST, the extension for metagenomic datasets, and Icarus, interactive visualizer for these tools.

References:

Documentation
Important Notes

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

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive --gres lscratch:10
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 quast
[+] Loading quast, version 5.0.2...
[user@cn3144 ~]$ cd /lscratch/$SLURM_JOB_ID
[user@cn3144 ~]$ quast.py --threads 2 \
    $QUAST_HOME/test_data/contigs_{1,2}.fasta \
    -R $QUAST_HOME/test_data/reference.fasta.gz \
    -G $QUAST_HOME/test_data/genes.gff 

[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. quast.sh). For example:

#!/bin/bash
set -e
module load quast

test -n "$SLURM_CPUS_PER_TASK" || SLURM_CPUS_PER_TASK=2

quast.py --threads $SLURM_CPUS_PER_TASK \
    $QUAST_HOME/test_data/contigs_{1,2}.fasta \
    -R $QUAST_HOME/test_data/reference.fasta.gz \
    -G $QUAST_HOME/test_data/genes.gff

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] quast.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. quast.swarm). For example:

quast.py $QUAST_HOME/test_data/contigs_{1,2}.fasta \
         -R $QUAST_HOME/test_data/reference.fasta.gz \
         -G $QUAST_HOME/test_data/genes.gff
quast.py $QUAST_HOME/test_data/contigs_{1,2}.fasta \
         -R $QUAST_HOME/test_data/reference.fasta.gz \
         -G $QUAST_HOME/test_data/genes.gff
quast.py $QUAST_HOME/test_data/contigs_{1,2}.fasta \
         -R $QUAST_HOME/test_data/reference.fasta.gz \
         -G $QUAST_HOME/test_data/genes.gff

Submit this job using the swarm command.

swarm -f quast.swarm [-g #] -t # --module quast
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 quast Loads the QUAST module for each subjob in the swarm