Biowulf High Performance Computing at the NIH
Sambamba on Biowulf

Sambamba is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files. Current parallelised functionality is an important subset of samtools functionality, including view, index, sort, markdup, and depth.


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 --cpus-per-task=4 --gres=lscratch:10
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 sambamba
[user@cn3144 ~]$ mkdir -p /data/$USER/sambamba && cd /data/$USER/sambamba
[user@cn3144 ~]$ cp $SAMBAMBA_TEST_DATA/* .
[user@cn3144 ~]$ sambamba sort -t $SLURM_CPUS_PER_TASK --tmpdir=lscratch/$SLURM_JOB_ID issue_204.bam
[user@cn3144 ~]$ sambamba view -t $SLURM_CPUS_PER_TASK -c -F "proper_pair" issue_204.bam
[user@cn3144 ~]$ 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. For example:

set -e
module load sambamba
sambamba sort -t $SLURM_CPUS_PER_TASK --tmpdir=lscratch/$SLURM_JOB_ID issue_204.bam

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=4 --gres=lscratch:10
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. sambamba.swarm). For example:

cd dir1; sambamba view --reference-info issue_204.bam
cd dir2; sambamba view --header --format=json issue_204.bam
cd dir3; sambamba flagstat -t $SLURM_CPUS_PER_TASK --show-progress issue_204.bam 

Submit this job using the swarm command.

swarm -f sambamba.swarm -t 4 --module sambamba
-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