Biowulf High Performance Computing at the NIH
steme on Biowulf

STEME started life as an approximation to the Expectation-Maximisation algorithm for the type of model used in motif finders such as MEME. STEME’s EM approximation runs an order of magnitude more quickly than the MEME implementation for typical parameter settings. STEME has now developed into a fully-fledged motif finder in its own right.


  • John E. Reid and Lorenz Wernisch. STEME: efficient EM to find motifs in large data sets. Nucleic Acids Research 2011(39): e126. Pubmed |  PMC |  Journal
  • John E. Reid and Lorenz Wernisch. STEME: a robust, accurate motif finder for large data sets. PLoS One 2014(13): e90735. Pubmed |  PMC |  Journal
Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144]$ cp ${STEME_TEST_DATA:-none}/* .
[user@cn3144]$ steme --minw=8 --maxw=8 --output-dir=./test1 \
  --write-em-stats T00759-small.fa
[user@cn3144]$ steme --min-sites=10 --bg-model-order=4 --use-seed=TCTGTGTTTGCATT \
  --bg-fasta-file=SOX2-t=20.fasta --prediction-Z-threshold=1e-10 \
  --output-dir=./test2 \

[user@cn3144]$ exit
salloc.exe: Relinquishing job allocation 46116226

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g., which uses the input file ''. For example:

#! /bin/bash

function fail {
    echo "$@" >&2
    exit 1

module load steme/1.9.1 || fail "could not load steme module"
cp $STEME_TEST_DATA/ctcf_*.fa .
steme --output-dir=./steme-ctcf --bg-fasta-file=ctcf_nonpeaks_random500.fa \
  --bg-model-order=4 ctcf_peaks_random500.fa

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=2
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

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

steme --output-dir=./result1 --bg-fasta-file=bg.fa exp1.fa
steme --output-dir=./result2 --bg-fasta-file=bg.fa exp2.fa
steme --output-dir=./result3 --bg-fasta-file=bg.fa exp3.fa

Submit this job using the swarm command.

swarm -f steme.swarm --module steme/1.9.1
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
-t # Number of threads/CPUs required for each process (1 line in the swarm command file).
--module steme Loads the steme module for each subjob in the swarm