java.lang.NullPointerException: Cannot invoke "beast.base.evolution.tree.Node.getNr()" because "<local7>" is null

[CiaccioE]

Hello,

I am trying to run an FBD dating analysis with StarBEAST3 (1.1.9) on BEAST 2.7.5 and I keep having an error I cannot find anywhere on google groups or github. I'm not sure what this error is pointing to. I have done divergence dating with this dataset using a Yule model, however I want to try an FBD model now.

I have attached my XML file (as .txt, for some reason github is not happy with XML)

Hypo6_run5_test.xml.txt

The error is a NullPointerException error as the title states. Any help would be greatly appreciated! Thanks,

Erik

java.lang.NullPointerException: Cannot invoke "beast.base.evolution.tree.Node.getNr()" because "" is null
at starbeast3.evolution.speciation.GeneTreeForSpeciesTreeDistribution.update(Unknown Source)
at starbeast3.evolution.speciation.GeneTreeForSpeciesTreeDistribution.mapGeneNodeToSpeciesNode(Unknown Source)
at starbeast3.core.StarBeastStartState.resetGeneTreeTipHeights(Unknown Source)
at starbeast3.core.StarBeastStartState.initStateNodes(Unknown Source)
at beast.base.inference.MCMC.run(Unknown Source)
at beastfx.app.beast.BeastMCMC.run(Unknown Source)
at beastfx.app.beast.BeastMain.main(Unknown Source)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.base/java.lang.reflect.Method.invoke(Unknown Source)
at beast.pkgmgmt.launcher.BeastLauncher.run(Unknown Source)
at beast.pkgmgmt.launcher.BeastLauncher.main(Unknown Source)

[rbouckaert]

@CiaccioE it looks like there is an alignment for the fossil that only has a single taxon (namely Cretacattyma_raveni_fossil1_gene). As a consequence, a tree with 1 node is created, which leads to the problem.

To fix this, the sequence alignment must be extended with a single sequence for Cretacattyma_raveni_fossil1_gene with all sites unknown (question marks) before importing into BEAUti. I edited the XML you posted and removed all references to the gene tree with only the Cretacattyma_raveni_fossil1_gene in it, and it seems to have solved the problem.

Hypo6_run5_test.xml.txt

Cheers, Remco

[CiaccioE]

Ahh ok that makes sense. I have it running as well, thank you very much Remco!!! Beast2 rocks

Erik

[rbouckaert]

Great to hear that, Erik!
I'll close the issue then, but you can reopen if the problem reappears.