Smrtpipe.log error: java.lang.outofmemoryerror: java heap space

The "java.lang.outofmemoryerror: java heap space" error is a common java error that occurs when the SW 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:

$SEYMOUR_HOME/analysis/bin/motifMaker.sh where the command-line java call is java -Xmx4000m -jar ${SEYMOUR_HOME}/analysis/lib/java/motif-maker-0.1.one-jar.jar $@ || exit $? and the default is 4Gb

And

$SEYMOUR_HOME/analysis/lib/python2.7/pbpy-0.1-py2.7.egg/pbpy/smrtpipe/modules/P_GATKVC.py where the default is also 4Gb “-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 and re-run the program. The java -Xms variable stands for initial heap size and the -Xmx stands for maximum heap size.