Biowulf High Performance Computing at the NIH
Breakdancer on HPC

The BreakDancer package provides genome-wide detection of structural variants from next generation paired-end sequencing reads.

Program breakdancer-max predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing reads using read pairs that are mapped with unexpected separation distances or orientation.


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 breakdancer
[user@cn3144 ~]$ bam_file1 bam_file2 %BreakdancerOptions% > config_file.cfg
[user@cn3144 ~]$ breakdancer-max config_file.cfg > file.ctx

[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. For example:

set -e
module load breakdancer
breakdancer-max config_file.cfg > file.ctx

Submit this job using the Slurm sbatch command.

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; breakdancer-max config_file.cfg > file.ctx
cd dir2; breakdancer-max config_file.cfg > file.ctx
cd dir3; breakdancer-max config_file.cfg > file.ctx

Submit this job using the swarm command.

swarm -f job.swarm --module breakdancer
-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 Loads the module for each subjob in the swarm