High-Performance Computing at the NIH
GitHub YouTube @nih_hpc RSS Feed
Bamliquidator on Biowulf

Bamliquidator is a set of tools for analyzing the density of short DNA sequence read alignments in the BAM file format

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
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 bamliqudiator

[user@cn3144 ~]$ bamliquidator sorted_and_indexed.bam chr1 0 100000 + 2 200
12345
67890

[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. bamliquidator.sh). For example:

#!/bin/bash
module load bamliquidator
bamliquidator_batch.py -n 16 -o test.output directory_of_bam_files/

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=16 --mem=10g bamliquidator.sh
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. bamliquidator.swarm). For example:

bamliquidator sorted_and_indexed.bam chr1 0 1000000 + 2 200
bamliquidator sorted_and_indexed.bam chr1 1000000 2000000 + 2 200
bamliquidator sorted_and_indexed.bam chr1 2000000 3000000 + 2 200
bamliquidator sorted_and_indexed.bam chr1 3000000 4000000 + 2 200

Submit this job using the swarm command.

swarm -f bamliquidator.swarm [-g 4] [-t 2] --module bamliquidator
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 bamliquidator Loads the bamliquidator module for each subjob in the swarm