Biowulf High Performance Computing at the NIH
ChromHMM on Biowulf

ChromHMM can segment genomes into different chromatin states by modeling re-occuring combinatorial and spatial pattern of various histone modifications with a multivariate Hidden Markov Model. The resulting segmentations can be used to annotate genomes. Bed files for immediate visualization in genome browsers are generated.

ChromHMM automatically computes state enrichments for functional and annotation datasets (TSSs, exons, ...) which facilitates the biological characterization of each state.

On Biowulf, ChromHMM can be run in two ways. The full path to the jarfile can be called like this:

java -mx4000M -Djava.awt.headless=true -jar $CHROMHMM_HOME/ChromHMM.jar [ command ] [ options ]
java -mx4000M -Djava.awt.headless=true -jar $CHROMHMM_JAR [ command ] [ options ]

The amount of memory is assigned with -mx[num], where 4000 MB is allocated. The second option -Djava.awt.headless=true is required, unless an X11 display is available. See here for more information about X11 display.

An easier way is to use the wrapper script This wrapper script includes an additional option to set the amount of memory: --memory 8g [ command ] [ options ]

By default, ChromHMM uses 4gb of memory. To allocate a different amount of memory, for example 20gb, include --memory 20g on the commandline.


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@biowulf]$ sinteractive --mem=8g --cpus-per-task=4 --gres=lscratch:10
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]$ cd /lscratch/$SLURM_JOB_ID
[user@cn3144]$ module load ChromHMM
[user@cn3144]$ cp -R $CHROMHMM_TEST_DATA/SAMPLEDATA_HG18 .
[user@cn3144]$ # train a model with 8 States; leave some buffer between memory given to JVM and
               # allocated memory
[user@cn3144]$ --memory 7g LearnModel -p $SLURM_CPUS_PER_TASK SAMPLEDATA_HG18 out 8 hg18
[user@cn3144]$ cp -r out /data/user/where/you/want/your/chromhmm/results

[user@cn3144]$ exit
salloc.exe: Relinquishing job allocation 46116226

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g., which uses the input file ''. For example:

#! /bin/bash

function fail() {
    echo "$@" >&2
    exit 1
module load ChromHMM/1.20 || fail "could not load module ChromHMM"
cd /lscratch/$SLURM_JOB_ID || fail "could not use lscratch"
cp -R $CHROMHMM_TEST_DATA/SAMPLEDATA_HG18 . --memory 8g LearnModel -p ${SLURM_CPUS_PER_TASK} \

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=8 --mem=9g
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. ChromHMM.swarm). For example: --memory 8g LearnModel -p ${SLURM_CPUS_PER_TASK} \
  SAMPLEDATA_HG18 OUTPUTSAMPLE8 8 hg18 --memory 8g LearnModel -p ${SLURM_CPUS_PER_TASK} \
  SAMPLEDATA_HG18 OUTPUTSAMPLE10 10 hg18 --memory 8g LearnModel -p ${SLURM_CPUS_PER_TASK} \

Submit this job using the swarm command.

swarm -f ChromHMM.swarm -g 9 -t 4 --module ChromHMM/1.20
-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 ChromHMM Loads the ChromHMM module for each subjob in the swarm