High-Performance Computing at the NIH
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Sortmerna on NIH HPC Systems

SortMeRNA: a sequence analysis tool for filtering, mapping and OTU-picking NGS reads.

On Helix

Sample session:

[susanc@helix ~]$ module load sortmerna
[susanc@helix ~]$ sortmerna -h

  Program:     SortMeRNA version 2.1, 01/02/2016
  Copyright:   2012-16 Bonsai Bioinformatics Research Group:
               LIFL, University Lille 1, CNRS UMR 8022, INRIA Nord-Europe
               2014-16 Knight Lab, Department of Pediatrics, UCSD, La Jolla,
  Disclaimer:  SortMeRNA comes with ABSOLUTELY NO WARRANTY; without even the
               implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
               See the GNU Lesser General Public License for more details.
  Contact:     Evguenia Kopylova, jenya.kopylov@gmail.com 
               Laurent Noé, laurent.noe@lifl.fr
               H幨鋝e Touzet, helene.touzet@lifl.fr

  usage:   ./sortmerna --ref db.fasta,db.idx --reads file.fa --aligned base_name_output [OPTIONS]:

Batch job on Biowulf

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

module load sortmerna

cd /data/$USER/dir
module load sortmerna
sormerna --ref db.fasta,db.idx --reads file.fa --aligned base_name_output

Then submit the file on biowulf

sbatch sortmerna.sh
Swarm of Jobs on Biowulf

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

# this file is called sormerna.swarm
cd dir1;sormerna command
cd dir2;sormerna command
cd dir3;sormerna command

Submit this job using the swarm command.

swarm -f sortmerna.swarm --module sortmerna

Interactive job on Biowulf
Allocate an interactive session and run raremetal. Sample session:
[susanc@biowulf ~]$ sinteractive 
salloc.exe: Pending job allocation 15194042
salloc.exe: job 15194042 queued and waiting for resources
salloc.exe: job 15194042 has been allocated resources
salloc.exe: Granted job allocation 15194042
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn1719 are ready for job

[susanc@cn1719 ~]$ module load sortmerna

[susanc@cn1719 ~]$ sormerna command