Biowulf High Performance Computing at the NIH
RaptorX on Biowulf

RaptorX is a protein structure prediction server developed by Xu group, excelling at predicting 3D structures for protein sequences without close homologs in the Protein Data Bank (PDB). Given an input sequence, RaptorX predicts its secondary and tertiary structures as well as solvent accessibility and disordered regions.

References:

Documentation
Important Notes

RaptorX uses psiblast, which can utilize multiple cpus to accelerate alignments.

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 --cpus-per-task=8
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 raptorx

[user@cn3144 ~]$ cp $RAPTORX_EXAMPLES/lysozyme .
[user@cn3144 ~]$ run_raptorx-ss3.pl lysozyme

[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. raptorx.sh). For example:

#!/bin/bash
module load raptorx
run_raptorx-ss8.pl blah.fasta

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=8 raptorx.sh
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. raptorx.swarm). For example:

run_raptorx-ss8.pl protein1.fasta
run_raptorx-ss8.pl protein2.fasta
run_raptorx-ss8.pl protein3.fasta
run_raptorx-ss8.pl protein4.fasta

Submit this job using the swarm command.

swarm -f raptorx.swarm [-g #] [-t #] --module raptorx
where
-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 raptorx Loads the raptorx module for each subjob in the swarm