Smrtpipe.log error: java.lang.outofmemoryerror: java heap space - dyim42/SMRT-Analysis GitHub Wiki

The java.lang.outofmemoryerror: java heap space error is a common Java error that occurs when the software does not allocate sufficient memory prior to running. (http://stackoverflow.com/questions/1596009/java-lang-outofmemoryerror-java-heap-space). Memory requirements for some Java programs are hard-coded in some of the SMRT Analysis scripts, for example:

referenceUploader

The script $SEYMOUR_HOME/analysis/bin/referenceUploader contains the command-line java call:

java -jar ${SEYMOUR_HOME}/analysis/lib/java/secondary-analysis-referenceUploader.jar where there is no

default memory allocation.

MotifMaker.sh

The script $SEYMOUR_HOME/analysis/bin/motifMaker.sh contains the command-line java call:

java -Xmx4000m -jar ${SEYMOUR_HOME}/analysis/lib/java/motif-maker-0.1.one-jar.jar $@ || exit $?

where the default memory allocation is 4 Gb.

GATKVC.py

The script $SEYMOUR_HOME/analysis/lib/python2.7/pbpy-0.1-py2.7.egg/pbpy/smrtpipe/modules/P_GATKVC.py contains the command-line java call:

java -Xmx4g -Djava.io.tmpdir=%s

where the default is also 4 Gb: “-Xmx4g”.

The hard-coded memory limit can be different for every application, and depending on how much memory you have on each node, you can increase this value and rerun the program. The Java -Xms variable stands for initial heap size, and -Xmx stands for maximum heap size.