Java error running StarBeast2

[Shea]

Hello, I'm attempting to run the newest version of StarBeast2 (0.13).

I first updated the package, then made my xml file. When I try to run it in BEAST, however, I get the following error message:

"Loading package BEAST v2.4.3
Loading package starbeast2 v0.13.0
java.lang.IllegalArgumentException: Input 'childModel' must be specified.
    at beast.core.Input.validate(Unknown Source)
    at beast.core.BEASTInterface.validateInputs(Unknown Source)
    at beast.util.XMLParser.createObject(Unknown Source)
    at beast.util.XMLParser.parseInputs(Unknown Source)
    at beast.util.XMLParser.createObject(Unknown Source)
    at beast.util.XMLParser.parseInputs(Unknown Source)
    at beast.util.XMLParser.createObject(Unknown Source)
    at beast.util.XMLParser.parseRunElement(Unknown Source)
    at beast.util.XMLParser.parse(Unknown Source)
    at beast.util.XMLParser.parseFile(Unknown Source)
    at beast.app.BeastMCMC.parseArgs(Unknown Source)
    at beast.app.beastapp.BeastMain.main(Unknown Source)
    at beast.app.beastapp.BeastLauncher.main(Unknown Source)

Error 110 parsing the xml input file

nullvalidate and intialize error: Input 'childModel' must be specified.

Error detected about here:
  <beast>
      <run id='mcmc' spec='MCMC'>
          <init id='SBI' spec='starbeast2.StarBeastInitializer'>
              <populationModel id='popModelBridge.Species' spec='starbeast2.PassthroughModel'>
"


Thanks for any advice,
Shea Lambert

[Huw A. Ogilvie]

Hi Shea,

This seems to happen if alignment files are dragged-and-dropped into the "Partitions" tab, instead of using the "+" button to add alignments. Can you try again using the "+" button and see if that fixes the issue?

- Huw

[Shea]

Hi Huw,

Indeed, I had drag-and-dropped the alignment.

Using the "+", I no longer get the childModel error, but I'm getting a new error:

"StarBEAST2: using fullInit to initialize all trees.
Fatal exception: Cannot find taxon 1 in data
java.lang.RuntimeException: Cannot find taxon 1 in data
    at beast.math.distributions.MRCAPrior.initialise(Unknown Source)
    at beast.math.distributions.MRCAPrior.calculateLogP(Unknown Source)
    at beast.core.util.CompoundDistribution.calculateLogP(Unknown Source)
    at beast.core.util.CompoundDistribution.calculateLogP(Unknown Source)
    at beast.core.State.robustlyCalcPosterior(Unknown Source)
    at beast.core.MCMC.run(Unknown Source)
    at beast.app.BeastMCMC.run(Unknown Source)
    at beast.app.beastapp.BeastMain.<init>(Unknown Source)

    at beast.app.beastapp.BeastMain.main(Unknown Source)
    at beast.app.beastapp.BeastLauncher.main(Unknown Source)

Fatal exception: Cannot find taxon 1 in data
java.lang.RuntimeException: An error was encounted. Terminating BEAST
    at beast.app.util.ErrorLogHandler.publish(Unknown Source)
    at java.util.logging.Logger.log(Logger.java:738)
    at java.util.logging.Logger.doLog(Logger.java:765)
    at java.util.logging.Logger.log(Logger.java:788)
    at java.util.logging.Logger.severe(Logger.java:1463)
    at beast.app.beastapp.BeastMain.<init>(Unknown Source)

    at beast.app.beastapp.BeastMain.main(Unknown Source)
    at beast.app.beastapp.BeastLauncher.main(Unknown Source)"

Thanks,
Shea

[Huw A. Ogilvie]

Hi Shae,

Could you attach the XML file so I can take a look at your MRCA calibrations?