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
- Module Name: bam2fastq (see the modules page for more information)
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 bam2fastqwhere
| -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 |