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vsearch
Overview
vsearch is a sequence analysis tool.
Version 1.1.3 is installed on the CSF.
Restrictions on use
This software may be used by all users, it is open-source.
Set up procedure
To access the software you must first load the modulefile:
module load apps/binapps/vsearch/1.1.3
Running the application
Please do not run vsearch on the login node. Jobs should be submitted to the compute nodes via batch.
Serial batch job submission
Make sure you have the modulefile loaded then create a batch submission script, for example:
#!/bin/bash #$ -S /bin/bash #$ -cwd # Job will run from the current directory #$ -V # Job will inherit current environment settings vsearch113 -cluster_fast combined.fasta -id 0.97 -uc results.uc -centroids centroids.fasta
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Parallel batch job submission
Make sure you have the modulefile loaded then create a batch submission script, for example:
#!/bin/bash #$ -S /bin/bash #$ -cwd # Job will run from the current directory #$ -V # Job will inherit current environment settings #$ -pe smp.pe 6 # Use 6 cores in smp.pe. The number six will be passed to $NSLOTS # which is used to tell usearch how many threads to use. vsearch113 -cluster_fast combined.fasta -id 0.97 --threads=$NSLOTS -uc results.uc -centroids centroids.fasta
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Further info
Updates
None.