Biowulf High Performance Computing at the NIH
Presto on HPC

pRESTO performs all stages of raw sequence processing prior to alignment against reference germline sequences. The toolkit is intended to be easy to use, but some familiarity with commandline applications is expected. Rather than providing a fixed solution to a small number of common workflows, we have designed pRESTO to be as flexible as possible. This design philosophy makes pRESTO suitable for many existing protocols and adaptable to future technologies, but requires users to construct a sequence of commands and options specific to their experimental protocol.


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@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 presto
[user@cn3144 ~]$ presto commands

[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:

set -e
module load presto
presto command

Submit this job using the Slurm sbatch command.

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. job.swarm). For example:

cd dir1; presto command
cd dir2; presto command
cd dir3; presto command

Submit this job using the swarm command.

swarm -f job.swarm --module presto
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
--module Loads the module for each subjob in the swarm