Biowulf High Performance Computing at the NIH
Cnvnator on HPC

CNVnator is a tool for CNV discovery and genotyping from depth of read mapping.

 

Paper

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 cnvnator
[user@cn3144 ~]$ cnvnator -root Output.root -tree Input.bam
[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 cnvnator
cnvnator -root Output.root -tree Input.bam

Submit this job using the Slurm sbatch command.

sbatch 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; cnvnator -root Output.root -tree Input.bam
cd dir2; cnvnator -root Output.root -tree Input.bam
cd dir3; cnvnator -root Output.root -tree Input.bam

Submit this job using the swarm command.

swarm -f job.swarm --module cnvnator
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