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

Platforms

• CIRCE cluster

Running MEME jobs on CIRCE

Modules

Meme requires the following module file and some prerequisites to run:

• apps/meme/3.5.7

• Prerequisites:
  • compilers/pgi/7.0-7.x86_64
  • openmpi/1.2.6-x86_64-pgi-7.0-7

See Modules for more information.

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. For help on submitting jobs to the queue, see our SLURM User’s Guide. Scripts are provided as examples only. Your SLURM executables, tools, and options will vary.

#!/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

More Job Information

See the following for more detailed job submission information:

• SLURM User’s Guide
• Scheduling and Dispatch Policies
• Advanced Submit Techniques

Reporting Bugs

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