Mothur

Description

From the Mothur home page: Mothur seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. We have incorporated the functionality of dotur, sons, treeclimber, s-libshuff, unifrac, and much more. In addition to improving the flexibility of these algorithms, we have added a number of other features including calculators and visualization tools.

Version

  • 1.42.3

Authorized Users

  • CIRCE account holders
  • SC account holders

Platforms

  • CIRCE cluster
  • SC cluster

Modules

Mothur requires the following module file to run:

  • apps/mothur/1.42.3

Running Mothur on CIRCE/SC

The Mothur user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations. Please refer to the Documentation section for a link to the guide.

  • Note on CIRCE: Make sure to run your jobs from your $WORK directory!
  • Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.

Submitting a Job

Use a submit script like the following to run Mothur:

#!/bin/bash
#
#SBATCH --job-name=mothur-test
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --mem-per-cpu=4096
#SBATCH --output=output.%j.mothur-test
#SBATCH --time=08:00:00

#### SLURM single node Mothur test 
#### to run for 8 hours 
#### using 1 processor core and 4 GB of memory

module purge
module add apps/mothur/1.42.3

mothur batchfile

 

Next, be sure that you are in your job’s directory, and run the sbatch command to submit the job:

[user@login0 ~]$ cd my/jobdir
[user@login0 jobdir]$ sbatch ./mothur-test.sh
  • You can view the status of your job with the “squeue -u <username>” command

Documentation

Home Page, User Guides, and Manuals

Benchmarks, Known Tests, Examples, Tutorials, and Other Resources


More Job Information

See the following for more detailed job submission information:

Reporting Bugs

Report bugs with Mothur to the IT Help Desk: rc-help@usf.edu