Biowulf High Performance Computing at the NIH
alleleCount on Biowulf

AlleleCount provides support code for NGS copy number algorithms. It exists primarily to prevent code duplication between some other projects, specifically AscatNGS and Battenburg. The project contains 2 equivalent implementations of allele counting code in perl and C for BAM/CRAM processing.

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 alleleCount

[user@cn3144 ~]$ cp $ALLELECOUNT_TEST_DATA/loci_22.txt .

[user@cn3144 ~]$ cp $ALLELECOUNT_TEST_DATA/test.bam* .

[user@cn3144 ~]$ alleleCounter -l loci_22.txt -b test.bam -o test.out
Reading locis
Done reading locis

[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
cd /data/$USER/mydir
module load alleleCount
alleleCounter -l loci.txt -b input.bam -o output.txt

Submit this job using the Slurm sbatch command.

sbatch [--mem=#]
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. alleleCount.swarm). For example:

alleleCounter -l loci1.txt -b input.bam -o output1.txt
alleleCounter -l loci2.txt -b input.bam -o output2.txt

Submit this job using the swarm command.

swarm -f alleleCount.swarm [-g #] --module alleleCount
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
--module alleleCount Loads the alleleCount module for each subjob in the swarm