Pilon is a application to improve draft assemblies and find variation among strains, including large event detection.

References:

• Bruce J. Walker, Thomas Abeel, Terrance Shea, Margaret Priest, Amr Abouelliel, Sharadha Sakthikumar, Christina A. Cuomo, Qiandong Zeng, Jennifer Wortman, Sarah K. Young, Ashlee M. Earl. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. . PLoS One. 2014 Nov 19;9(11).

• pilon Main Site: GitHub

• Module Name: pilon (see the modules page for more information)
• Limit memory usage with the java heap size option -Xmx (e.g. -Xmx16g for 16 GB).
• Environment variables set: PILON_HOME, PILON_JAR
• Note that to be able to use the environment variable SLURM_MEM_PER_NODE below, you will need to explicitly allocate memory resources.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --cpus-per-task=4 --mem=4g
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 cn4224 are ready for job

[user@cn4224 ~]$ module load pilon
[+] Loading pilon  1.23 

[user@cn4224 ~]$ java -Xmx${SLURM_MEM_PER_NODE}m -jar $PILON_JAR --genome genome.fasta --frags frag.sorted.bam --ouput OUTPUT --vcf
Pilon version 1.23 Mon Dec 21 10:00:01 2020 -0600
[...]

[user@cn4224 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226

[user@biowulf ~]$

Create a batch input file (e.g. pilon.sh) similar to the following.

#! /bin/bash

set -e

module load pilon

java -Xmx${SLURM_MEM_PER_NODE}m -jar ${PILON_JAR} --genome genome.fasta --frags frag.sorted.bam --ouput OUTPUT --vcf

Submit these jobs using the Slurm sbatch command.

Create a swarmfile for the first step of the pipeline (e.g. pilon.swarm). For example:

java -Xmx${SLURM_MEM_PER_NODE}m -jar ${PILON_JAR}  --genome genome.fasta --frags frag00.sorted.bam --ouput OUTPUT --vcf
java -Xmx${SLURM_MEM_PER_NODE}m -jar ${PILON_JAR}  --genome genome.fasta --frags frag02.sorted.bam --ouput OUTPUT --vcf
java -Xmx${SLURM_MEM_PER_NODE}m -jar ${PILON_JAR}  --genome genome.fasta --frags frag03.sorted.bam --ouput OUTPUT --vcf

Submit this job using the swarm command.

swarm -f pilon.swarm [-g #] --module pilon