Biowulf High Performance Computing at the NIH
SCRATCH-1D on Biowulf

SCRATCH-1D is a suite of one-dimensional predictors included in the long-established and widely used SCRATCH suite of predictors developed by the Institute for Genomics and Bioinformatics (IGB) of the University of California, Irvine (UCI).

SCRATCH-1D currently includes the following predictors and tools:

References:

Documentation
Important Notes

SCRATCH-1D requires local scratch space for temporary files. Please include --gres=lscratch:N with job submissions, with N being the number of GB required. Typically 10 or less is adequate.

SCRATCH-1D is multithreaded, but multiple threads are only necessary if the input fasta file has multiple sequences.

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 --mem-per-cpu=4g --gres=lscratch:10
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 scratch1d

[user@cn3144 ~]$ ml scratch1d
[user@cn3144 ~]$ cp ${SCRATCH1D_EXAMPLES}/test.fasta .
[user@cn3144 ~]$ run_SCRATCH-1D_predictors.sh test.fasta test.out ${SLURM_CPUS_ON_NODE}

[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. scratch1d.sh). For example:

#!/bin/bash
set -e
module load scratch1d
run_SCRATCH-1D_predictors.sh test.fasta test.out ${SLURM_CPUS_ON_NODE}

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] scratch1d.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. scratch1d.swarm). For example:

run_SCRATCH-1D_predictors.sh prot1.fasta prot1.out 1
run_SCRATCH-1D_predictors.sh prot2.fasta prot2.out 1
run_SCRATCH-1D_predictors.sh prot3.fasta prot3.out 1
run_SCRATCH-1D_predictors.sh prot4.fasta prot4.out 1

In this case, each fasta contains 1 sequence, so the number of threads required is 1.

Submit this job using the swarm command.

swarm -f TEMPLATE.swarm -g # -t # --module scratch1d
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 scratch1d Loads the scratch1d module for each subjob in the swarm