BEAST2 gives errors when using BEAGLE

[Alexandra Gavryushkina]

 Hi beast2 team, 

I am running a beast2 analysis with morphological data (so BEAGLE might not be needed in my case). The analysis runs but gives the following errors for each of the alignements. 

What is this error about? Also is there a way to tell beast2 to not use beagle? 

Using BEAGLE version: 4.0.0 (PRE-RELEASE) resource 0: CPU (x86_64)

    with instance flags:  PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU

  Ignoring ambiguities in tree likelihood.

  Ignoring character uncertainty in tree likelihood.

  With 73 unique site patterns.

  Using rescaling scheme : dynamic

java.lang.NullPointerException: Cannot invoke "beast.base.evolution.substitutionmodel.EigenDecomposition.getEigenVectors()" because "<local2>" is null

at beast.base.evolution.likelihood.BeagleTreeLikelihood.setUpSubstModel(Unknown Source)

at beast.base.evolution.likelihood.BeagleTreeLikelihood.initialize(Unknown Source)

at beast.base.evolution.likelihood.BeagleTreeLikelihood.initAndValidate(Unknown Source)

at beast.base.core.BEASTInterface.initByName(Unknown Source)

at beast.base.evolution.likelihood.TreeLikelihood.initAndValidate(Unknown Source)

at beast.base.parser.XMLParser.initBEASTObjects(Unknown Source)

at beast.base.parser.XMLParser.parse(Unknown Source)

at beast.base.parser.XMLParser.parseFile(Unknown Source)

at beastfx.app.beast.BeastMCMC.parseArgs(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)

TreeLikelihood(morphTreeLikelihood.canidae2) uses BeerLikelihoodCore

  FilteredAlignment(canidae2): [taxa, patterns, sites] = [225, 73, 73]

[Jo Baker]

Dear Alex, 

This is the exact message I'm receiving when trying to run the example code from this recent paper (Zhang et al 2024 Syst Biol): 

https://datadryad.org/stash/dataset/doi:10.5061/dryad.pnvx0k6vj

Did you find any solution to this or figure out what exactly was the problem - as the analysis seems to still run.

Best wishes, 

Jo 

[Alexandra "Sasha" Gavryushkina]

Hi Jo,

Nope, I didn't solve this problem. 

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[Artem B]

Hi Sasha,

Unchecking this box disables BEAGLE. It's strange since the problem usually arises with the use of the BEAGLE library, not the other way.

Best wishes,
Artem

среда, 20 ноября 2024 г. в 01:18:57 UTC+8, Alexandra "Sasha" Gavryushkina: