Biowulf High Performance Computing at the NIH
JAMM on Biowulf

JAMM is a peak finder for NGS datasets (ChIP-Seq, ATAC-Seq, DNase-Seq..etc.) that can integrate replicates and assign peak boundaries accurately. JAMM is applicable to both broad and narrow datasets.

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 --cpus-per-task=16 --mem=8g
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 JAMM
[user@cn3144 ~]$ JAMM.sh -p ${SLURM_CPUS_PER_TASK} -s /path/to/sample/files -g genome_size_file.txt -o /path/to/output -c /path/to/input/files

[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. JAMM.sh). For example:

#!/bin/bash
module load JAMM
JAMM.sh \
  -p ${SLURM_CPUS_PER_TASK} \
  -s /path/to/sample/files \
  -g genome_size_file.txt \
  -o /path/to/output \
  -c /path/to/input/files

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=16 --mem=8g JAMM.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. JAMM.swarm). For example:

JAMM.sh -p ${SLURM_CPUS_PER_TASK} -s /path/to/sample/files1 \
  -g genome_size_file.txt -o /path/to/output1 -c /path/to/input/files1
JAMM.sh -p ${SLURM_CPUS_PER_TASK} -s /path/to/sample/files2 \
  -g genome_size_file.txt -o /path/to/output2 -c /path/to/input/files2
JAMM.sh -p ${SLURM_CPUS_PER_TASK} -s /path/to/sample/files3 \
  -g genome_size_file.txt -o /path/to/output3 -c /path/to/input/files3
JAMM.sh -p ${SLURM_CPUS_PER_TASK} -s /path/to/sample/files4 \
  -g genome_size_file.txt -o /path/to/output4 -c /path/to/input/files4

Submit this job using the swarm command.

swarm -f JAMM.swarm -g 8 -t 16 --module JAMM
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 JAMM Loads the JAMM module for each subjob in the swarm