Biowulf High Performance Computing at the NIH
Rilseq on HPC

This package can be used to analyzed RILseq experiments. It is written for a prokaryotic genome, without splice junction mapping and with some additional features. The package handles the different stages processing fastq files to pairs of interacting RNAs and some statistics. It does not handle quality issues, adapter removing etc. so the fastq files should be treated with cutadapt or equivalent before applying this package.


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 rilseq
[user@cn3144 ~]$ rilseq command

[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 rilseq
rilseq command

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. job.swarm). For example:

cd dir1;rilseq command 1; rilseq command 2
cd dir2;rilseq command 1; rilseq command 2
cd dir3;rilseq command 1; rilseq command 2

Submit this job using the swarm command.

swarm -f job.swarm [-t #] --module rilseq
-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