Biowulf High Performance Computing at the NIH
PePr on Biowulf

PePr is a ChIP-Seq Peak-calling and Prioritization pipeline that uses a sliding window approach and models read counts across replicates and between groups with a negative binomial distribution. PePr empirically estimates the optimal shift/fragment size and sliding window width, and estimates dispersion from the local genomic area. Regions with less variability across replicates are ranked more favorably than regions with greater variability. Optional post-processing steps are also made available to filter out peaks not exhibiting the expected shift size and/or to narrow the width of peaks.

References:

Documentation
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
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 PePr
[user@cn3144 ~]$ cp $PEPR_EXAMPLES/* .
[user@cn3144 ~]$ PePr -i input_rep1.bed,input_rep2.bed -c chip_rep1.bed,chip_rep2.bed -f bed -s 45 -w 180 -n my_test_run

[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. PePr.sh). For example:

#!/bin/bash
module load PePr
PePr -c SRR446029_1.fastq_trim.gz.bam,SRR446030_1.fastq_trim.gz.bam \
  --chip2 SRR446031_1.fastq_trim.gz.bam,SRR446032_1.fastq_trim.gz.bam -f bam --diff -s 10

Submit this job using the Slurm sbatch command.

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

PePr -c ex1_A.bam,ex1_B.bam --chip2 ex2_A.bam,ex2_B.bam -f bam --diff -n ex1_ex2
PePr -c ex1_A.bam,ex1_B.bam --chip2 ex3_A.bam,ex3_B.bam -f bam --diff -n ex1_ex3
PePr -c ex1_A.bam,ex1_B.bam --chip2 ex4_A.bam,ex4_B.bam -f bam --diff -n ex1_ex4
PePr -c ex1_A.bam,ex1_B.bam --chip2 ex5_A.bam,ex5_B.bam -f bam --diff -n ex1_ex5

Submit this job using the swarm command.

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