yass is a genomic similarity seach tool for nucleic (and only nucleic) sequences in (multi)fasta or plain text format. yass produces local pairwise alignments in yass format, blast tabular format, or PSL format.

References:

• Noe L., Kucherov G. YASS: enhancing the sensitivity of DNA similarity search. Nucleic Acids Research, 2005 33(2):W540-W543. doi:10.1093/nar/gki478

• YASS Main Site
• YASS on GitHub

• Module Name: yass (see the modules page for more information)

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 yass

[user@cn3144 ~]$ yass file1.fa file2.mfa > yass-output.yop 

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. yass.sh). For example:

#!/bin/bash
set -e
module load yass
yass file1.fa file2.mfa > yass-output.yop

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] yass.sh

Create a swarmfile (e.g. yass.swarm). For example:

yass file1a.fa file1b.mfa > yass-output1.yop
yass file2a.fa file2b.mfa > yass-output2.yop
yass file3a.fa file3b.mfa > yass-output3.yop

Submit this job using the swarm command.

swarm -f yass.swarm [-g #] [-t #] --module yass