Biowulf High Performance Computing at the NIH
Rscape on Biowulf

R-scape looks for evidence of a conserved RNA structure by measuring pairwise covariations observed in an input multiple sequence alignment. It analyzes all possible pairs, including those in your proposed structure (if you provide one). R-scape uses a null hypothesis that takes phylogenetic correlations and base composition biases into account, which can be sources of apparent pairwise covariation that are not due to conserved RNA structure.


Important Notes
Submitting an interactive job

Allocate an interactive session and run the interactive job there.

[biowulf]$ sinteractive --mem=5g
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 rscape

[cn0135]$ cp -rp /usr/local/apps/rscape/1.5.2/tutorial .
[cn0135]$ cd tutorial
[cn0135]$ R-scape -s updated_Arisong.sto

[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salloc.exe: Job allocation 789523 has been revoked.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 rscape || exit 1
cd /data/$USER/tutorial
R-scape -s updated_Arisong.sto

2. Submit the script on biowulf:

[biowulf]$ sbatch --mem=5g 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/$USER/dir1; R-scape -s updated_Arisong.sto
cd /data/$USER/dir2; R-scape -s updated_Arisong.sto
cd /data/$USER/dir3; R-scape -s updated_Arisong.sto
cd /data/$USER/dir20; R-scape -s updated_Arisong.sto

submit the swarm job:

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

For more information regarding running swarm, see swarm.html