MUSIC is an algorithm for identification of enriched regions at multiple scales in the read depth signals from ChIP-Seq experiments.
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/ Preprocessing: Input Format: SAM ChIP-Seq input file path: stdin Parsed Reads Output Directory: chip/ Added 1 Added 2 Added 3 Added 4 Added 5 Added 6 Added 7 Added 8 Added 9 Added 10 Added 11 Added 12 Added 13 Added 14 Added 15 Added 16 Added 17 Added 18 Added 19 Added X Added M MUSIC finished preprocessing SAM formatted reads in 59 seconds. [user@cn3144 ~]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$
Create a batch input file (e.g. music.sh). For example:
#!/bin/bash set -e module load music samtools view 1.bam | MUSIC -preprocess SAM stdin chip/
Submit this job using the Slurm sbatch command.
sbatch music.sh
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 musicwhere
--module music | Loads the music module for each subjob in the swarm |