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Breakdancer on Biowulf

Breakdancer provides genome-wide detection of structural variants from next generation paired-end sequencing reads. BreakDancerMax 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.

Programs location

/usr/local/apps/breakdancer/current

 

The environment variable(s) need to be set properly first. The easiest way to do this is by using the modules commands as in the example below.

$ module avail breakdancer
----------------------------- /usr/local/Modules/3.2.9/modulefiles --------------------------
breakdancer/1.1.2(default) breakdancer/1.1_2011_02_21

$ module load breakdancer

$ module list
Currently Loaded Modulefiles:
  1) breakdancer/1.1.2
$ module unload breakdancer $ module load breakdancer/1.1.2 $ module show breakdancer ------------------------------------------------------------------- /usr/local/Modules/3.2.9/modulefiles/breakdancer/1.1.2: module-whatis Sets up breakdancer 1.1.2 prepend-path PATH /usr/local/apps/breakdancer/1.1.2/cpp prepend-path PATH /usr/local/apps/breakdancer/1.1.2/perl -------------------------------------------------------------------

Sample Sessions On Biowulf

Submitting a single breakdancer batch job

1. Create a script file alone the lines below.

#!/bin/bash
# This file is runFile
#
#PBS -N breakdancer
#PBS -m be
#PBS -k oe

module load breakdancer
cd /data/$USER/breakdancer/run1
bam2cfg.pl bam_file1 bam_file2 breakdancer_options > config_file.cfg
breakdancer-max config_file.cfg > file.ctx

3. Submit the script using the 'qsub' command on Biowulf

$ qsub -l nodes=1:g8 /data/$USER/runFile

 

Submitting a swarm of breakdancer jobs

Using the 'swarm' utility, one can submit many jobs to the cluster to run concurrently.

Set up a swarm command file (eg /data/$USER/cmdfile). Here is a sample file:

cd /data/$USER/Dir1; bam2cfg.pl bam_file1 bam_file2 breakdancer_options>config_file.cfg; breakdancer-max config_file.cfg>file.ctx 
cd /data/$USER/Dir2; bam2cfg.pl bam_file1 bam_file2 breakdancer_options>config_file.cfg; breakdancer-max config_file.cfg>file.ctx 
[.....]
cd /data/$USER/Dir20; bam2cfg.pl bam_file1 bam_file2 breakdancer_options>config_file.cfg; breakdancer-max config_file.cfg>file.ctx 

The '-f' and '--module' options for swarm are required

By default, each line of the command file above will be executed on 1 processor core of a node and use 1gb of memory. If this is not what you want, you will need to specify '-g' flags when you submit the job on biowulf. Say if each line of the commands above need to use 10gb of memory instead of the default 1gb of memory, make sure swarm understands this by including '-g 10' flag:

biowulf> $ swarm -g 10 -f swarmFile --module breakdancer

For more information regarding running swarm, see swarm.html

 

Submit an interactive breakdancer job

1. To do so, user first allocate a node from the cluster then run commands interactively on the node. DO NOT RUN ON BIOWULF LOGIN NODE:

$ qsub -I -l nodes=1:g8

or if your job require bigger memory,

$ qsub -I -l nodes=1:g24:c16

2. Once the job started and a node is allocated, run the interactive commands.

$ module load breakdancer
$ cd /data/$USER/breakdancer/run1
$ bam2cfg.pl bam_file1 bam_file2 breakdancer_options>config_file.cfg
$ breakdancer-max config_file.cfg>file.ctx 
  

 

Documentation

http://gmt.genome.wustl.edu/breakdancer/1.2/documentation.html