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:
- Ibrahim MM, Lacadie SA, Ohler U. JAMM: a peak finder for joint analysis of NGS replicates Bioinformatics. 2015 Jan 1;31(1):48-55.
Documentation
Important Notes
- Module Name: JAMM (see the modules page for more information)
- Multithreaded
- Environment variables set
- PATH
- JAMM_EXAMPLES -- example files
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 ~]$ cp $JAMM_EXAMPLES/testdata.zip . [user@cn3144 ~]$ unzip testdata.zip [user@cn3144 ~]$ JAMM.sh -s testdata -g testdata/chrSizes21.csize -o JAMM.results -p $SLURM_CPUS_ON_NODE [user@cn3144 ~]$ [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 JAMMwhere
-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 |