PSIPRED on Biowulf
PSIPRED generates secondary structure predictions using up to four feed-forward neural networks and output from PSI-BLAST.
References:
- Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. (1999) 292: 195-202.
Documentation
Important Notes
- Module Name: PSIPRED (see the modules page for more information)
- Multithreaded
- Environment variables set
- PSIPRED_HOME
- PSIPRED_EXAMPLES
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=4 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 PSIPRED [user@cn3144 ~]$ cp $PSIPRED_EXAMPLES/example.fasta . [user@cn3144 ~]$ runpsipredplus example.fasta Running PSI-BLAST with sequence example.fasta ... Predicting secondary structure... Pass1 ... Pass2 ... Cleaning up ... Final output files: example.ss2 example.horiz Finished. [user@cn3144 ~]$ ls example.fasta example.horiz example.ss example.ss2 [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. PSIPRED.sh). For example:
#!/bin/bash module load PSIPRED runpsipredplus my.fasta
Submit this job using the Slurm sbatch command.
sbatch [--cpus-per-task=#] [--mem=#] PSIPRED.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. PSIPRED.swarm). For example:
runpsipredplus file1.fasta > run1.out runpsipredplus file2.fasta > run2.out runpsipredplus file3.fasta > run3.out runpsipredplus file4.fasta > run4.out
Submit this job using the swarm command.
swarm -f PSIPRED.swarm [-g #] [-t #] --module PSIPREDwhere
-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 PSIPRED | Loads the PSIPRED module for each subjob in the swarm |