java.lang.NullPointerException at initialization

[zhangchicool]

At the beginning of the run, BEAST2 shows:
java.lang.NullPointerException
at beast.evolution.likelihood.BeagleTreeLikelihood.setUpSubstModel(BeagleTreeLikelihood.java:474)
at beast.evolution.likelihood.BeagleTreeLikelihood.initialize(BeagleTreeLikelihood.java:364)
at beast.evolution.likelihood.BeagleTreeLikelihood.initAndValidate(BeagleTreeLikelihood.java:99)
at beast.core.BEASTInterface.initByName(BEASTInterface.java:105)
at beast.evolution.likelihood.TreeLikelihood.initAndValidate(TreeLikelihood.java:132)
at beast.util.XMLParser.initBEASTObjects(XMLParser.java:377)
at beast.util.XMLParser.parse(XMLParser.java:535)
at beast.util.XMLParser.parseFile(XMLParser.java:302)
at beast.app.BeastMCMC.parseArgs(BeastMCMC.java:311)
at beast.app.BeastMCMC.main(BeastMCMC.java:567)

although the run will continue and will have results.
A toy xml will reproduce the problem:
test.xml.zip

[SimonGreenhill]

BEAGLE can't handle the datatype, a workaround is to disable beagle with the -java flag. This is very slow though

[zhangchicool]

The xml was generated by BEAUti, and I seem to notice this exception only recently