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Biobambam2 on Biowulf
Description

This package contains some tools for processing BAM files including

Documentation
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 --mem=10g --cpus-per-task=4
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 biobambam2
[user@cn3144 ~]$ bamsort inputthreads=$SLURM_CPUS_PER_TASK SO=queryname < in.bam > out.bam 

[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. script.sh), which uses the input file 'file.in'. For example:

#!/bin/bash
module load biobambam2
bamsort inputthreads=$SLURM_CPUS_PER_TASK SO=queryname < in.bam > out.bam

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=4 --mem=10g script.sh
Swarm of Jobs
A swarm of jobs is an easy way to submit set of independent commands requiring identical resources.

Create a swarmfile (e.g. biobambam2.swarm). For example:

bamsort inputthreads=$SLURM_CPUS_PER_TASK SO=queryname < in1.bam > out1.bam
bamsort inputthreads=$SLURM_CPUS_PER_TASK SO=queryname < in2.bam > out2.bam
bamsort inputthreads=$SLURM_CPUS_PER_TASK SO=queryname < in3.bam > out3.bam

Submit this job using the swarm command.

swarm -f biobambam2.swarm -g 10 -t 4 --module biobambam2
where
-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 biobambam2 Loads the biobambam2 module for each subjob in the swarm