Issue Thorney-beast with relax clock model #1217

AlbertoA3 · 2025-02-04T18:31:31Z

Dear BEAST-developers.

At this point I available to running a XML-file using a Thorney-BEAST with a relax clock-model with around 2500 taxas on the assay. However when I try using the Thorney-BEAST with a relax clock-model using more than 7000 taxas the following error emerge from the assay

BEAST v1.10.5 Prerelease #a6fb, 2002-2019
Bayesian Evolutionary Analysis Sampling Trees
Designed and developed by
Alexei J. Drummond, Andrew Rambaut and Marc A. Suchard

           Department of Computer Science
               University of Auckland
              [email protected]
                          
         Institute of Evolutionary Biology
              University of Edinburgh
                 [email protected]
                          
          David Geffen School of Medicine
       University of California, Los Angeles
                 [email protected]
                          
            Downloads, Help & Resources:
              	http://beast.community

Source code distributed under the GNU Lesser General Public License:
http://github.com/beast-dev/beast-mcmc

                 BEAST developers:
Alex Alekseyenko, Guy Baele, Trevor Bedford, Filip Bielejec, Erik Bloomquist, Matthew Hall,
Joseph Heled, Sebastian Hoehna, Denise Kuehnert, Philippe Lemey, Wai Lok Sibon Li,
Gerton Lunter, Sidney Markowitz, Vladimir Minin, Michael Defoin Platel,
      	Oliver Pybus, Chieh-Hsi Wu, Walter Xie
                          
                     Thanks to:
	Roald Forsberg, Beth Shapiro and Korbinian Strimmer

Using BEAGLE library v4.0.0 (PRE-RELEASE) for accelerated, parallel likelihood evaluation
2009-, BEAGLE Working Group - https://beagle-dev.github.io/
Citation: Ayres et al (2019) Systematic Biology 68: 1052-1061 | doi:10.1093/sysbio/syz020

Random number seed: 1738690810091

Failed to load parser: New parser (gmrfSkygridBlockUpdateOperator) in {interface dr.inference.operators.MCMCOperator} cannot replace existing parser (gmrfSkygridBlockUpdateOperator) in {interface dr.inference.operators.MCMCOperator}
line = dr.evomodelxml.coalescent.operators.GMRFSkygridBlockUpdateOperatorParser

Failed to load parser: dr.evomodelxml.coalescent.GMRFTestLikelihoodParser
line = dr.evomodelxml.coalescent.GMRFTestLikelihoodParser

Failed to load parser: dr.inference.trace.DnDsPerSiteAnalysis
line = dr.inference.trace.DnDsPerSiteAnalysis

Failed to load parser: dr.inference.trace.CnCsPerSiteAnalysis
line = dr.inference.trace.CnCsPerSiteAnalysis

Failed to load parser: dr.inference.trace.CnCsToDnDsPerSiteAnalysis
line = dr.inference.trace.CnCsToDnDsPerSiteAnalysis

Loading additional development parsers from development_parsers.properties, which is additional set of parsers only available for development version ...

Failed to load parser: dr.evomodel.continuous.hmc.TaskPool
line = dr.evomodel.continuous.hmc.TaskPool

Failed to load parser: dr.inferencexml.operators.RepeatOperatorParser
line = dr.inferencexml.operators.RepeatOperatorParser

Parsing XML file: RC-3T-S2-1.xml
File encoding: UTF8
Looking for plugins in /Users/albertoaguayoacosta/Desktop/BEAST-version/BEASTv1.10.5pre_thorney_0.1.2-3/bin/plugins
Using node heights.

Creating the constrained tree model based on big fast tree model, 'treeModel'
taxon count = 7039
tree height = 5.622136535735911
The gmrfSkyrideLikelihood has time aware smoothing
Creating a GMRF smoothed skyride model for multiple loci (SkyGrid)
Population sizes: 33

Using discretized relaxed clock model.
over sampling = 1
parametric model = logNormalDistributionModel
rate categories = 1
Creating swap operator for parameter branchRates.categories (weight=10.0)
Optimization Schedule: log
Creating CTMC Scale Reference Prior model.
Acting on subtree of size 7039

Likelihood computation is using an auto sizing thread pool.

Creating the MCMC chain:
chain length = 100000000
operator adaption = true
adaptation delayed for 1000000 steps
WARNING: Likelihood component, skygrid.precision.prior, created but not used in the MCMC
WARNING: Likelihood component, branchRates, created but not used in the MCMC
Feb 04, 2025 11:40:11 AM dr.app.beast.BeastMain
SEVERE: Error running file: RC-3T-S2-1.xml
Feb 04, 2025 11:40:11 AM dr.app.beast.BeastMain
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)=(
CTMCScalePrior(ctmcScalePrior)=10.0707,
Exponential(ucld.stdev)=0.0986,
Gamma(skygrid.precision)=-4.6139,
GMRFSkygridLikelihood(gmrfSkyrideLikelihood[skygrid])=-45836726.4454
Total = -4.583672088999632E7
),
CompoundLikelihood(compoundModel)=(
ThorneyTreeLikelihood(thorneyTreeLikelihood[treeLikelihood])=-Inf
Total = -Infinity
)
Total = -Infinity
For more information go to http://beast.community.

However, I would like to mention a peculiar situation, trying several time to use the same XML-file one of the running was avialabe to start and Im not really sure what cause these behavior on my files and running.

I attach the message of the running that was available to proceed

     BEAST v1.10.5 Prerelease #a6fb, 2002-2019
   Bayesian Evolutionary Analysis Sampling Trees
             Designed and developed by

Alexei J. Drummond, Andrew Rambaut and Marc A. Suchard

           Department of Computer Science
               University of Auckland
              [email protected]
                          
         Institute of Evolutionary Biology
              University of Edinburgh
                 [email protected]
                          
          David Geffen School of Medicine
       University of California, Los Angeles
                 [email protected]
                          
            Downloads, Help & Resources:
              	http://beast.community

Source code distributed under the GNU Lesser General Public License:
http://github.com/beast-dev/beast-mcmc

                 BEAST developers:
Alex Alekseyenko, Guy Baele, Trevor Bedford, Filip Bielejec, Erik Bloomquist, Matthew Hall,
Joseph Heled, Sebastian Hoehna, Denise Kuehnert, Philippe Lemey, Wai Lok Sibon Li,
Gerton Lunter, Sidney Markowitz, Vladimir Minin, Michael Defoin Platel,
      	Oliver Pybus, Chieh-Hsi Wu, Walter Xie
                          
                     Thanks to:
	Roald Forsberg, Beth Shapiro and Korbinian Strimmer

Using BEAGLE library v4.0.0 (PRE-RELEASE) for accelerated, parallel likelihood evaluation
2009-, BEAGLE Working Group - https://beagle-dev.github.io/
Citation: Ayres et al (2019) Systematic Biology 68: 1052-1061 | doi:10.1093/sysbio/syz020

Random number seed: 1738690644144