Cnvnator on HPC
CNVnator is a tool for CNV discovery and genotyping from depth of read mapping.
Paper
Documentation
- Module Name: cnvnator(see the modules page for more information)
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 -chrom 1 2 [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 cnvnatorwhere
| -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 |