Biowulf High Performance Computing at the NIH
Ceas on Biowulf

CEAS is a tool designed to characterize genome-wide protein-DNA interaction patterns from ChIP-chip and ChIP-Seq of both sharp and broad binding factors. It provides statistics on ChIP enrichment at important genome features such as specific chromosome, promoters, gene bodies, or exons, and infers genes most likely to be regulated by a binding factor. CEAS also enables biologists to visualize the average ChIP enrichment signals over specific genomic features, allowing continuous and broad ChIP enrichment to be perceived which might be too subtle to detect from ChIP peaks alone.

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 ~]$module load ceas

[user@cn3144 ~]$ cd /data/$USER/ceas

[user@cn3144 ~]$ cp /fdb/CEAS/* .

[user@cn3144 ~]$ ceas --name=H3K36me3_ceas --pf-res=20 --gn-group-names='Top 10%,Bottom 10%' \
  -g /fdb/CEAS/hg18.refGene -b H3K36me3_MACS_pval1e-5_peaks.bed -w H3K36me3.wig

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

Batch job
Most jobs should be run as batch jobs.

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

module load ceas
cd /data/$USER/ceas
ceas --name=H3K36me3_ceas --pf-res=20 --gn-group-names='Top 10%,Bottom 10%'\
  -g /fdb/CEAS/hg18.refGene -b H3K36me3_MACS_pval1e-5_peaks.bed -w H3K36me3.wig

Submit this job using the Slurm sbatch command.

sbatch --mem=#10g
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. ceas.swarm). For example:

  cd /data/$USER/dir1; ceas commands
  cd /data/$USER/dir2; ceas commands
  cd /data/$USER/dir3; ceas commands

Submit this job using the swarm command.

swarm -f ceas.swarm -g 10 --module ceas
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
--module ceas Loads the ceas module for each subjob in the swarm