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:

TMP_DIR=/lscratch/$SLURM_JOBID

Then submit with:

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

or

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

Replace ? above with memory in GB

• http://broadinstitute.github.io/picard/

• Module Name: picard (see the modules page for more information)
• Multithreaded
environment variables set
• $PICARDJARPATH - path to the directory holding the jar file(s)
• $PICARD_JARPATH - path to the directory holding the jar file(s)
• $PICARDJAR - for versions > 1.119, the path to the single picard jar file
• $PICARD_JAR - for versions > 1.119, the path to the single picard jar file

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 ~]$

Create a batch input file (e.g. batch.sh). For example:

#!/bin/bash
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

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