Biowulf High Performance Computing at the NIH
Music (CHIPseq Peak Caller) on Biowulf

MUSIC is an algorithm for identification of enriched regions at multiple scales in the read depth signals from ChIP-Seq experiments.

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 music

[user@cn3144 ~]$ mkdir chip

[user@cn3144 ~]$ samtools view /usr/local/apps/macs/TEST_DATA/ENCFF001NGB.bam | MUSIC -preprocess SAM stdin chip/
Input Format: SAM
ChIP-Seq input file path: stdin
Parsed Reads Output Directory: chip/
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MUSIC finished preprocessing SAM formatted reads in 59 seconds.

[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 music
samtools view 1.bam | MUSIC -preprocess SAM stdin chip/

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. music.swarm). For example:

samtools view 1.bam | MUSIC -preprocess SAM stdin chip1/
samtools view 2.bam | MUSIC -preprocess SAM stdin chip2/
samtools view 3.bam | MUSIC -preprocess SAM stdin chip3/

Submit this job using the swarm command.

swarm -f music.swarm --module music
--module music Loads the music module for each subjob in the swarm