Biowulf High Performance Computing at the NIH
bam2fastq on HPC

BAM-format files are used to store alignment information and unaligned reads from next-generation sequencing machines. This tool is intended to extract raw sequences (with qualities) from a BAM file.

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 bam2fastq
[user@cn3144 ~]$ bam2fastq input.bam -o outfile#
[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. bam2fastq.sh). For example:

#!/bin/bash
set -e
module load bam2fastq
bam2fastq input.bam -o outfile#

Submit this job using the Slurm sbatch command.

sbatch bam2fastq.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. bam2fastq.swarm). For example:

cd dir1; bam2fastq input.bam -o outfile#
cd dir2; bam2fastq input.bam -o outfile#
cd dir3; bam2fastq input.bam -o outfile#

Submit this job using the swarm command.

swarm -f bam2fastq.swarm [-t #] --module bam2fastq
where
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
--module Loads the module for each subjob in the swarm