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 SLURM and to include this option when starting your batch job (the SLURM system will enforce the 1 user limit):

#SBATCH -L usearch@osc:1
Non-interactive Batch Job

Use the script below as a template for your usage.

#!/bin/bash
#SBATCH -t 1:00:00
#SBATCH --nodes=1 --ntask-per-node=28
#SBATCH -L usearch@osc:1
#SBATCH --job-name=usearch

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

Further Reading

Supercomputer: 
Owens