Prodigal

Prodigal is a program to perform fast, reliable protein-coding gene prediction for prokaryotic genomes.

Version 2.6.3 is installed on the CSF. It has been compiled with the gcc and intel compilers.

Restrictions on use

There are no restrictions on accessing the software on the CSF. It is released under the GNU GPL v3 license and all usage should adhere to that license.

Set up procedure

To access the software you must first load one of the following modulefiles:

module load apps/gcc/prodigal/2.6.3

# The intel compiler version may be faster.
module load apps/intel-15.0/prodigal/2.6.3

Running the application

Please do not run prodigal on the login node. Jobs should be submitted to the compute nodes via batch. You may run on the login node:

prodigal -h

to see a list of command-line flags accepted by the application.

Serial batch job submission

Prodigal is a serial application only. Make sure you have the modulefile loaded then create a batch submission script, for example:

#!/bin/bash
#$ -S /bin/bash
#$ -cwd             # Job will run from the current directory
#$ -V               # Job will inherit current environment settings

prodigal arg1 arg2 ... 

Submit the jobscript using:

qsub scriptname

where scriptname is the name of your jobscript.

Further info

• Prodigal website

Updates

None.