EDD on Biowulf

EDD is a ChIP-seq peak caller for detection of megabase domains of enrichment.


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 input in bold):

[user@biowulf]$ sinteractive --cpus-per-task=8
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 edd
[user@cn3144 ~]$ ln -s $EDD_EXAMPLES/hg19.sizes .
[user@cn3144 ~]$ ln -s $EDD_EXAMPLES/*.bam .
[user@cn3144 ~]$ touch unalign.bed
[user@cn3144 ~]$ edd -p $SLURM_CPUS_PER_TASK -n 10000 hg19.sizes unalign.bed SRX447385.bam SRX447386.bam output_dir

[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. edd.sh). For example:


# Generate hg19 chrom sizes
module load ucsc
fetchChromSizes hg19 > hg19.sizes
module unload ucsc

# Create empty file for unalignable regions
touch unalign_empty

# Run the command, collecing output in output directory
ml edd
edd -p $SLURM_CPUS_PER_TASK -n 10000 hg19.sizes unalign.bed chip_seq.bam input.bam output_dir

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] edd.sh
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. edd.swarm). For example:

edd -p $SLURM_CPUS_PER_TASK hg19.sizes unalign.bed chip_seq_1.bam input_1.bam output_dir_1
edd -p $SLURM_CPUS_PER_TASK hg19.sizes unalign.bed chip_seq_2.bam input_2.bam output_dir_2
edd -p $SLURM_CPUS_PER_TASK hg19.sizes unalign.bed chip_seq_3.bam input_3.bam output_dir_3
edd -p $SLURM_CPUS_PER_TASK hg19.sizes unalign.bed chip_seq_4.bam input_4.bam output_dir_4

Submit this job using the swarm command.

swarm -f edd.swarm [-g #] [-t #] --module edd
-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 edd Loads the edd module for each subjob in the swarm