Picard on HPC

Picard comprises Java-based command-line utilities that manipulate SAM files, and a Java API (SAM-JDK) for creating new programs that read and write SAM files. Both SAM text format and SAM binary (BAM) format are supported.

Picard changed a bit back to a single jar, so currently picard command lines look like this:

   java [java opts] -jar $PICARDJARPATH/picard.jar command [options]
   java -jar $PICARDJARPATH/picard.jar --help

Note 1

MarkDuplicates tends to initiate garbage collection threads. It's suggested that users add -XX:ParallelGCThreads=5 in the picard command and request 6 cpus for the command (1 for picard, 5 for garbage collection)

java -Xmx???g -XX:ParallelGCThreads=5 -jar $PICARDJARPATH/picard.jar MarkDuplicates ........

Note 2

For tools that can generate lots of temperatory files (such as FastqToSam), or when error message 'slurmstepd: Exceeded job memory limit at some point' appears, it's suggested to include this flag to the picard command:


Then submit with:

sbatch --cpus-per-task=6 --mem=?g --gres=lscratch:200


swarm -f swarmfile -t 6 -g ? --gres=lscratch:200

Replace ? above with memory in GB

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 --cpus-per-task=5
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 picard
[user@cn3144 ~]$ java -Xmx4g -XX:ParallelGCThreads=5 -jar $PICARDJARPATH/picard.jar command [options]

[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. batch.sh). For example:

set -e
module load picard
java -Xmx4g -XX:ParallelGCThreads=5 -jar $PICARDJARPATH/picard.jar command [options]

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=6 batch.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. job.swarm). For example:

cd dir1; java -Xmx4g -XX:ParallelGCThreads=5 -jar $PICARDJARPATH/picard.jar command [options]
cd dir2; java -Xmx4g -XX:ParallelGCThreads=5 -jar $PICARDJARPATH/picard.jar command [options]
cd dir3; java -Xmx4g -XX:ParallelGCThreads=5 -jar $PICARDJARPATH/picard.jar command [options]
cd dir4; java -Xmx4g -XX:ParallelGCThreads=5 -jar $PICARDJARPATH/picard.jar command [options]

Submit this job using the swarm command.

swarm -f job.swarm -t 6 --module picard
-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 Loads the module for each subjob in the swarm