Biowulf High Performance Computing at the NIH
IntaRNA on Biowulf
IntaRNA is a program for the fast and accurate prediction of interactions between two RNA molecules. It has been designed to predict mRNA target sites for given non-coding RNAs (ncRNAs) like eukaryotic microRNAs (miRNAs) or bacterial small RNAs (sRNAs), but it can also be used to predict other types of RNA-RNA interactions. Precomputed results for Enterobacteria: ChiX, CyaR, FnrS, GcvB, MicC, RyhB, Spot42, and for Non-enteric bacteria: LhrA2, PrrF1, Yfr1.

Documentation

https://github.com/BackofenLab/IntaRNA/

Important Notes
Submitting an interactive job

Allocate an interactive session and run the interactive job there.

[biowulf]$ sinteractive --mem=10g --cpus-per-task=4
salloc.exe: Granted job allocation 789523
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn0135 are ready for job

[cn0135]$ cd /data/$USER/

[cn0135]$ module load intarna

[cn0135]$ cp -rp /usr/local/apps/intarna/*.fasta /data/$USER
[cn0135]$ IntaRNA -t target.fasta -q query.fasta


[cn0135]$ exit
salloc.exe: Job allocation 789523 has been revoked.

Submitting a single batch job

1. Create a script file (myscript) similar to the one below

#! /bin/bash
# myscript
set -e

module load intarna || exit 1
cd /data/$USER/
IntaRNA -t target.fasta -q query.fasta

2. Submit the script on biowulf:

[biowulf]$ sbatch --mem=5g -c 4 myscript

Using Swarm

Using the 'swarm' utility, one can submit many jobs to the cluster to run concurrently.

Set up a swarm command file (eg /data/$USER/cmdfile).

cd /data/$USER/dir1; IntaRNA -t target.fasta -q query.fasta
cd /data/$USER/dir2; IntaRNA -t target.fasta -q query.fasta
cd /data/$USER/dir3; IntaRNA -t target.fasta -q query.fasta
...
cd /data/$USER/dir20; IntaRNA -t target.fasta -q query.fasta

submit the swarm job:

$ swarm -f cmdfile --module intarna -g 5 -t 4

For more information regarding running swarm, see swarm.html