Infernal (“INFERence of RNA ALignment”) is for searching DNA sequence databases for RNA structure and sequence similarities. You can find more information about Infernal here.
To use Infernal the modules for its software and other dependencies need to be loaded first. The easiest way to do this is editing your
.bashrc file in your
$HOME directory, by adding the lines below. You may have to restart your session for this to take affect.
module load impi/5.0.0 module load gcc/4.9.1 module load infernal
Then in your
$HOME directory create a directory to submit your Infernal jobs from. Copy the tutorial folder, provided by Infernal, to the directory you just made in your
razor-l1:jokinsey:~$ mkdir INFERNAL-JOBS razor-l1:jokinsey:~$ cd INFERNAL-JOBS/ razor-l1:jokinsey:~/INFERNAL-JOBS$ cp -r /share/apps/bioinformatics/infernal/infernal-1.1.1-linux-intel-gcc/tutorial .
If you see a folder named
tutorial in the submission directory you created then you are ready to run the example.
In the submission directory for you Infernal jobs create a file named
infernal.pbs with the information below. This is a
PBS script that will be submitted to run the test job.
#!/bin/bash #PBS -N infernal #PBS -q tiny12core #PBS -j oe #PBS -o infernal.$PBS_JOBID #PBS -l nodes=1:ppn=12 #PBS -l walltime=0:05:00 cd $PBS_O_WORKDIR cp -r tutorial /scratch/$PBS_JOBID cd /scratch/$PBS_JOBID cmbuild tRNA5.cm tutorial/tRNA5.sto cmcalibrate --forecast tRNA5.cm cmcalibrate tRNA5.cm cmsearch -o tRNA5.cmsearch.out tRNA5.cm tutorial/mrum-genome.fa mkdir $PBS_O_WORKDIR/infernal.$PBS_JOBID cp -r . $PBS_O_WORKDIR/infernal.$PBS_JOBID
This script is first running
cmbuild to build a covariance model using the alignment file provided with the tutorial. Then using
cmcalibrate calculates the
e-values needed to search the database. Finally it searches the sequence database provided by the tutorial, and stores that output to the file
tRNA5.cmsearch.out. This tutorial follows the example provided by Infernal, which you can find here.
All that's left to do is submit the job.
razor-l1:jokinsey:~/INFERNAL-JOBS$ qsub infernal.pbs
You can find the output located in the folder
infernal.$PBS_JOBID. If you need to review the standard output when the job was ran, it will be located in the file