USEARCH

USEARCH is a sequence analysis tool that offers high-throughput search and clustering algorithms to analyze data.

Availability and Restrictions

Versions

USEARCH is available on the Owens cluster. The versions currently available at OSC are:

VERSION OWENS
10.0.240 X*
* Current Default Version

You can use module spider usearch to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access

USEARCH is available to all academic OSC users.

Publisher/Vendor/Repository and License Type

drive5, Commercial

Usage

Usage on Owens

Set-up

To configure your environment for use of USEARCH, use command module load usearch. This will load the default version.

Using USEARCH

Due to licensing restrictions, USEARCH may ONLY be used via the batch system on Owens. See below for information on how this is done.

Batch Usage

OSC has a 1-user license for USEARCH. However, there is no enforcement mechanism. In order for us to stay within the 1-user limit, we require you to run in the context of PBS and to include this option when starting your batch job (the PBS system will enforce the 1 user limit):

#PBS -l software=usearch
Interactive Batch Session

The following illustrates how to run USEARCH via an interactive batsh session. Please note that this requires an X11 server on the client system.

oakley01: qsub -X -I -l nodes=1:ppn=28 -l software=usearch 
qsub: waiting for job 5860.owens-batch.osc.edu to start
qsub: job 5860.owens-batch.osc.edu ready

n0533: module load usearch
n0533: usearch -cluster_fast data.fa -id 0.9 -centroids output.fa
n0533: exit
Non-interactive Batch Job

Use the script below as a template for your usage.

#PBS -l walltime=01:00:00
#PBS -l nodes=1:ppn=28
#PBS -l software=usearch
#PBS -N usearch
#PBS -j oe

module load usearch
cd $PBS_O_WORKDIR
# sample usearch command
usearch -cluster_fast data.fa -id 0.9 -centroids output.fa

Further Reading

Supercomputer: