Meme

Description

MEME allows discovery of motifs (highly conserved regions) in groups of related DNA or protein sequences.

Version

  • 3.5.7

Authorized Users

  • CIRCE account holders
  • SC account holders

Platforms

  • CIRCE cluster
  • SC cluster

Modules

Meme requires the following module file to run:

  • apps/meme/3.5.7

Running Meme on CIRCE/SC

The Meme 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

If, for example, you have an MEME input file named meme.in, you would set up a submit script like this:

  • The script below (for testing, name it “meme-test.sh”) can be copied into your job directory (the folder with your input files) and modified so that you can submit batch processes to the queue.
#!/bin/bash
#
#SBATCH --comment=meme-test
#SBATCH --ntasks=4
#SBATCH --job-name=meme-test
#SBATCH --output=output.%j.meme-test
#SBATCH --time=01:00:00

#### SLURM 4 processor MEME test to run for 1 hour.

module add apps/meme/3.5.7
mpirun /opt/apps/meme/bin/meme 

 
Next, you can change to your job’s directory, and run the sbatch command to submit the job:

[user@login0 ~]$ cd my/jobdir
[user@login0 jobdir]$ sbatch ./meme-test.sh

Documentation

Home Page, User Guides, and Manuals

More Job Information

See the following for more detailed job submission information:

Reporting Bugs

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