marginal likelihood estimation error

[Florencia Alvarez Gallego]

Hello everyone,
I’m using BEAST v2.7.8 with the Contraband v1.0.2 and Model Selection v1.6.2 packages to estimate marginal likelihoods with the stepping-stone (GSS) method.
I’m comparing four models to compare recombination in one species:
GSS_recomb_dates.log
GSS_recomb_noDates.log
GSS_const_dates.log
GSS_const_noDates.log

However, the runs stop immediately, and the following error appears in the log file:

WARNING: This model (tree prior) cannot handle dated tips. Please select a tree prior which can, otherwise results may be invalid.

NodeMath::Setting dimension of rho values to 6

NodeMath::Setting dimension of trait rate to 4.

Starting frequencies: [0.25, 0.25, 0.25, 0.25]

java.lang.NumberFormatException: For input string: "CTCA ... continues"

at java.base/jdk.internal.math.FloatingDecimal.readJavaFormatString(Unknown Source)

at java.base/jdk.internal.math.FloatingDecimal.parseDouble(Unknown Source)

at java.base/java.lang.Double.parseDouble(Unknown Source)

at contraband.prunelikelihood.PruneLikelihoodProcess.processContinuousAlignment(Unknown Source)

at contraband.prunelikelihood.PruneLikelihoodProcess.initAndValidate(Unknown Source)

at contraband.prunelikelihood.BMPruneLikelihood.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)

Error 110 parsing the xml input file

validate and intialize error: For input string: "CTCAACCCAG... continues"

Error detected about here:

  <beast>

      <run id='PathSampler' spec='modelselection.inference.PathSampler'>

          <mcmc id='mcmc' spec='MCMC'>

              <distribution id='posterior' spec='CompoundDistribution'>

                  <distribution id='likelihood' spec='CompoundDistribution'>

                      <distribution id='contTreeLikelihood.sp' spec='contraband.prunelikelihood.BMPruneLikelihood'>

Has anyone experienced this issue when running stepping-stone analyses ?  Could it be related to the alignment format or the XML setup of the model?

Any advice would be greatly appreciated.

Thanks in advance,
Florencia