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Pindel on HPC

Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.

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@biowulf]$ sinteractive
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 pindel
[user@cn3144 ~]$ cd /data/$USER/demo
[user@cn3144 ~]$ pindel -i simulated_config.txt -f simulated_reference.fa -o outfile -c ALL

[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. batch.sh). For example:

#!/bin/bash
set -e
module load pindel
pindel -i simulated_config.txt -f simulated_reference.fa -o outfile -c ALL

Submit this job using the Slurm sbatch command.

sbatch [--mem=#] batch.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. job.swarm). For example:

cd dir1; pindel -i simulated_config.txt -f simulated_reference.fa -o outfile -c ALL
cd dir2; pindel -i simulated_config.txt -f simulated_reference.fa -o outfile -c ALL

cd dir3; pindel -i simulated_config.txt -f simulated_reference.fa -o outfile -c ALL

Submit this job using the swarm command.

swarm -f job.swarm [-g #] --module pindel
where
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
--module Loads the module for each subjob in the swarm