USEARCH
Overview
USEARCH is a sequence analysis tool.
Versions 8.0.1623 and 11.0.667 (pre-compiled 32 bit binaries) are installed on the CSF.
USEARCH is often used with QIIME. These pieces of software are installed separately on the CSF. If you wish to use them together you need to load USEARCH and QIIME modulefiles (see below).
Restrictions on use
This software is not open source. We have been granted a free academic license for the CSF by the developer. All users must observe the license terms on the usearch website, a copy of which is also available in the install directory. In particular it should be noted that:
- The software is not to be used for commercial purposes.
- You must not copy or make the software available to anyone else.
- You must cite your usage of the software as per the citation information on the usearch website.
If you are unsure whether your usage complies with the terms please contact its-ri-team@manchester.ac.uk.
To use the software you must agree to the terms, by emailing your confirmation you have read the above information to its-ri-team@manchester.ac.uk, and then you can be added to the usearch unix group which controls access.
Set up procedure
We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this. Alternatively, you may load modulefiles on the login node and let the job inherit these settings.
To access the software you must first load one of the following modulefiles:
module load apps/binapps/usearch/11.0.667 module load apps/binapps/usearch/8.0.1623
If you wish to run QIIME please also load the following modulefiles:
module load apps/bioinf module load apps/qiime/1.9.1 # Use module search apps/qiime to check for newer versions
Running the application
Please do not run USEARCH 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 --login #$ -cwd # Job will run from the current directory ### We now load the modulefile in the jobscript, for example: module load apps/binapps/usearch/11.0.667 usearch -cluster_fast seqs.fasta -id 0.9 -centroids nr.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 --login #$ -cwd # Job will run from the current directory #$ -pe smp.pe 6 # Use 6 cores in smp.pe (2--32 permitted) ### We now load the modulefile in the jobscript, for example: module load apps/binapps/usearch/11.0.667 ### $NSLOTS is automatically set to number of cores requested above usearch -cluster_fast seqs.fasta -id 0.9 -threads $NSLOTS -centroids nr.fasta
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Further info
Updates
None.