Biowulf High Performance Computing at the NIH
PRANK on Biowulf

PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences. PRANK is based on a novel algorithm that treats insertions correctly and avoids over-estimation of the number of deletion events. In addition, PRANK borrows ideas from maximum likelihood methods used in phylogenetics and correctly takes into account the evolutionary distances between sequences. Lastly, PRANK allows for defining a potential structure for sequences to be aligned and then, simultaneously with the alignment, predicts the locations of structural units in the sequences.


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 input in bold):

[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 PRANK
[user@cn3144 ~]$ prank -d=input_file -t=tree_file -o=output_file -F -showxml

[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:

module load PRANK
prank -d=input_file -t=tree_file -o=output_file -F -showxml

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--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. PRANK.swarm). For example:

prank -d=input_file_1 -t=tree_file -o=output_file_1 -F -showxml
prank -d=input_file_2 -t=tree_file -o=output_file_2 -F -showxml
prank -d=input_file_3 -t=tree_file -o=output_file_3 -F -showxml
prank -d=input_file_4 -t=tree_file -o=output_file_4 -F -showxml

Submit this job using the swarm command.

swarm -f PRANK.swarm [-g #] [-t #] --module PRANK
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
-t # Number of threads/CPUs required for each process (1 line in the swarm command file).
--module PRANK Loads the PRANK module for each subjob in the swarm