Node prior not accepted by BEAUti?

[Abby Williams]

Hi, I'm struggling to understand why my node priors are not accepted by BEAST. 

I'm working in BEAUti v10.5.0 and noticed that my node priors are not being saved to the XML file. I would like to calibrate a node for which I have a minimum age of 24 mya. After adding the clade for which I want to set the minimum age in the 'taxa' tab, I then go to the 'prior' tab, set the distribution to lognormal and the following parameters: mu=1.5 sigma=1 offset=24. But after 'OK'-ing, this doesn't seem to have saved on the page, and neither does it appear correctly when I save the XML file.

I have tried manually overwriting the XML file output by changing this (the result of saving the file after attempting to add the prior):

    <!-- Define MCMC                                                             -->

    <mcmc id="mcmc" chainLength="10000000" autoOptimize="true" operatorAnalysis="aligned_with_partitions.ops.txt">

        <joint id="joint">

            <prior id="prior">

                <booleanLikelihood>

                    <monophylyStatistic idref="monophyly(columbidae)"/>

                </booleanLikelihood>

                <logNormalPrior mu="0.0" sigma="1.0" offset="0.0">

                    <statistic idref="tmrca(columbidae)"/>

To this:

    <!-- Define MCMC                                                             -->

    <mcmc id="mcmc" chainLength="10000000" autoOptimize="true" operatorAnalysis="aligned_with_partitions.ops.txt">

        <joint id="joint">

            <prior id="prior">

                <booleanLikelihood>

                    <monophylyStatistic idref="monophyly(columbidae)"/>

                </booleanLikelihood>

                <logNormalPrior mu="1.5" sigma="1.0" offset="24.0">

                    <statistic idref="tmrca(columbidae)"/>

But after attempting to run the edited file in BEAST, I get the following error, which makes me think that some of the values I'm setting are incompatible:

  Likelihood computation is using an auto sizing thread pool. Mar 19, 2026 12:11:12 PM dr.app.beast.BeastMain <init> SEVERE: Error running file: aligned_with_partitions.xml Mar 19, 2026 12:11:12 PM dr.app.beast.BeastMain <init> SEVERE: The initial model is invalid because state has a zero probability. If the log likelihood of the tree is -Inf, this may be because the initial, random tree is so large that it has an extremely bad likelihood which is being rounded to zero. Alternatively, it may be that the product of starting mutation rate and tree height is extremely small or extremely large. Finally, it may be that the initial state is incompatible with one or more 'hard' constraints (on monophyly or bounds on parameter values. This will result in Priors with zero probability. The individual components of the posterior are as follows: The initial posterior is zero: CompoundLikelihood(compoundModel)=( BooleanLikelihood=0.0, LogNormal(tmrca(pigeons))=-Inf, LogNormal(kappa)=-1.8654, MultivariateDistributionLikelihood(dirichletDistribution)=1.79 Creating the MCMC chain: chain length = 10000000 operator adaption = true adaptation delayed for 100000 steps 18, CTMCScalePrior(ctmcScalePrior)=-6.7031, Gamma(constant.popSize)=-6.9151, Gamma(subtree.constant.popSize)=-6.9151, CoalescentLikelihood(coalescentLikelihood[coalescent])=-0.477, CoalescentLikelihood(coalescentLikelihood[subtree.coalescent])=-10.4984, StrictClockBranchRates(strictClockBranchRates[branchRates])=0.0 Total = -Infinity ), CompoundLikelihood(compoundModel)=( TreeDataLikelihood(TreeDataLikelihood[treeLikelihood_1])=-29061.7351, TreeDataLikelihood(TreeDataLikelihood[treeLikelihood_1])=-36102.2895, TreeDataLikelihood(TreeDataLikelihood[treeLikelihood_1])=-1222.9505, TreeDataLikelihood(TreeDataLikelihood[treeLikelihood_1])=-2087.8546 Total = -68474.82973864823 ) Total = -Infinity For more information go to <http://beast.community>.  

I have tried the following:

• Setting a root height prior (lognormal distribution, mean 50, SD 1) - I have the same issue with it not saving to the XML file
• Unchecking the 'monophyly' box in the Taxa tab

But not sure what else I can try. I am new to BEAST so there may be gaps in my understanding, but any and all help is much appreciated!