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Cis-regulatory Element Annotation System 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.

 

Programs Location

/usr/local/ceas/bin

 

Environmental variable need to be set correctly first:

$ module load ceas

Submitting a Single Batch Job

1. Create a script file. The file will contain the lines similar to the lines below. Modify the path of location before running. Remember, the above environmental variables have to be set correctly first. The example files used below can be copied from /fdb/CEAS

#!/bin/bash
# This file is FileName
#
#PBS -N RunName
#PBS -m be
#PBS -k oe

module load ceas
cp /fdb/CEAS/H3K36me3_MACS_pval1e-5_peaks.bed /data/user/ceas/run1
cp /fdb/CEAS/H3K36me3.wig /data/user/ceas/run1
cd /data/user/ceas/run1 
ceas --name=H3K36me3_ceas --pf-res=20 --gn-group-names='Top 10%,Bottom 10%' -g hg18.refGene -b H3K36me3_MACS_pval1e-5_peaks.bed -w H3K36me3.wig

3. Submit the script using the 'qsub' command on Biowulf, e.g. Note, user is recommend to run benchmarks to determine what kind of node is suitable for his/her jobs.

qsub -l nodes=1 /data/user/theScriptFileAbove

Useful commands:

freen: see http://biowulf.nih.gov/user_guide.html#freen

qstat: search for 'qstat' on http://biowulf.nih.gov/user_guide.html for it's usage.

jobload: search for 'jobload' on http://biowulf.nih.gov/user_guide.html for it's usage.

 

Submitting a Swarm of Jobs

Using the 'swarm' utility, one can submit many jobs to the cluster to run concurrently.

Set up a swarm command file (eg /data/username/cmdfile). Here is a sample file:

module load ceas;\
cd /data/user/run1/; \
ceas command1 ;\
ceas command2

module load ceas ;\
cd /data/user/run2/; \
ceas command1 ;\
ceas command2

.........

module load ceas ;\
cd /data/user/runN/; \
ceas command1 ;\
ceas command2

There are one flag of swarm that's required '-f' and two other flags of swarm user most possibly needs to specify when submit a swarm job: '-t' and '-g'.

-f: the swarm command file name above (required)
-t: number of processors per node to use for each line of the commands in the swarm file above.(optional)
-g: GB of memory needed for each line of the commands in the swarm file above.(optional)

By default, each line of the commands above will be executed on '1' processor core of a node and uses 1GB of memory. If this is not what you want, you will need to specify '-t' and '-g' flags when you submit the job on biowulf.

Say if each line of the commands above also will need to use 10gb of memory instead of the default 1gb of memory, make sure swarm understands this by including '-g 10' flag:

biowulf> $ swarm -g 10 -f cmdfile

For more information regarding running swarm, see swarm.html

 

Running an Interactive Job

User may need to run jobs interactively sometimes. Such jobs should not be run on the Biowulf login node. Instead allocate an interactive node as described below, and run the interactive job there.

biowulf% qsub -I -l nodes=1
qsub: waiting for job 2236960.biobos to start
qsub: job 2236960.biobos ready

[user@p4]$ cd /data/user/myruns
[user@p4]$ module load ceas
[user@p4]$ cd /data/userID/run1
[user@p4]$ ceas command 1
[user@p4]$ ceas command 2
[user@p4]$ ...........
[user@p4] exit
qsub: job 2236960.biobos completed
[user@biowulf ~]$

User may add property of node in the qsub command to request specific interactive node. For example, if you need a node with 8gb of memory to run job interactively, do this:

biowulf% qsub -I -l nodes=1:g8

Documentation

http://liulab.dfci.harvard.edu/CEAS/