I ran a beast analysis implementing Shrinkage local clock model in BEAST Version v10.5.0-beta4 Prerelease. The analysis ran Ok and finished mcmc part but I got an error while it started to perform the path-sampling steps to estimate marginal likelihood.
Can I estimate path-sampling implementing Shrinkage local clock?
It looks like the error is relate to "Path parameter has no effect on Metropolis-Hastings kernels. Gibbs samplers need an implementation for use in power-posteriors"
The error is bellow.
WARNING: Likelihood component, substBranchRates, created but not used in the MCMC
Creating the Marginal Likelihood Estimator chain:
chainLength=1000000
pathSteps=100
pathScheme=betaQuantile(0.3)
Citations for this analysis:
FRAMEWORK
Marginal likelihood estimation using path sampling / stepping-stone sampling (first 2 citations) and generalized stepping-stone sampling (3rd citation):
Baele G, Lemey P, Bedford T, Rambaut A, Suchard MA, Alekseyenko AV (2012) Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty. Mol. Biol. Evol.. 29, 2157-2167
Baele G, Li WLS, Drummond AJ, Suchard MA, Lemey P (2013) Accurate model selection of relaxed molecular clocks in Bayesian phylogenetics. Mol. Biol. Evol.. 30, 239-243
Baele G, Lemey P, Suchard MA (2016) Genealogical working distributions for Bayesian model testing with phylogenetic uncertainty. Syst. Biol.. 65, 250-264
Attempting theta (1/101) = 1.0 for 1000000 iterations + 100000 burnin.
Exception in thread "Thread-1" java.lang.IllegalArgumentException: Path parameter has no effect on Metropolis-Hastings kernels.
Gibbs samplers need an implementation for use in power-posteriors
at dr.inference.operators.SimpleMCMCOperator.setPathParameter(Unknown Source)
at dr.inference.mcmc.MarginalLikelihoodEstimator.integrate(Unknown Source)
at dr.inference.mcmc.MarginalLikelihoodEstimator.run(Unknown Source)
at java.base/java.lang.Thread.run(Thread.java:840)
1 file(s) found with marginal likelihood samples
Loading log /home/jpons/Documents/chiara/13PCG_amphiclock_3part_BD_noG3rd_SLC_run2.mle.log ...
Oct 10, 2024 9:01:53 PM dr.app.beast.BeastMain
SEVERE:
Error in input BEAST XML file, 13PCG_amphiclock_3part_BD_noG3rd_SLC_run2.xml:
Error parsing '' element with id, 'null':
Incorrect file format, no sample is found !
I ran a beast analysis implementing Shrinkage local clock model in BEAST Version v10.5.0-beta4 Prerelease. The analysis ran Ok and finished mcmc part but I got an error while it started to perform the path-sampling steps to estimate marginal likelihood. Can I estimate path-sampling implementing Shrinkage local clock? It looks like the error is relate to "Path parameter has no effect on Metropolis-Hastings kernels. Gibbs samplers need an implementation for use in power-posteriors" The error is bellow.
WARNING: Likelihood component, substBranchRates, created but not used in the MCMC
Creating the Marginal Likelihood Estimator chain: chainLength=1000000 pathSteps=100 pathScheme=betaQuantile(0.3)
Citations for this analysis:
FRAMEWORK Marginal likelihood estimation using path sampling / stepping-stone sampling (first 2 citations) and generalized stepping-stone sampling (3rd citation): Baele G, Lemey P, Bedford T, Rambaut A, Suchard MA, Alekseyenko AV (2012) Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty. Mol. Biol. Evol.. 29, 2157-2167 Baele G, Li WLS, Drummond AJ, Suchard MA, Lemey P (2013) Accurate model selection of relaxed molecular clocks in Bayesian phylogenetics. Mol. Biol. Evol.. 30, 239-243 Baele G, Lemey P, Suchard MA (2016) Genealogical working distributions for Bayesian model testing with phylogenetic uncertainty. Syst. Biol.. 65, 250-264
Attempting theta (1/101) = 1.0 for 1000000 iterations + 100000 burnin. Exception in thread "Thread-1" java.lang.IllegalArgumentException: Path parameter has no effect on Metropolis-Hastings kernels. Gibbs samplers need an implementation for use in power-posteriors at dr.inference.operators.SimpleMCMCOperator.setPathParameter(Unknown Source) at dr.inference.mcmc.MarginalLikelihoodEstimator.integrate(Unknown Source) at dr.inference.mcmc.MarginalLikelihoodEstimator.run(Unknown Source) at java.base/java.lang.Thread.run(Thread.java:840) 1 file(s) found with marginal likelihood samples Loading log /home/jpons/Documents/chiara/13PCG_amphiclock_3part_BD_noG3rd_SLC_run2.mle.log ... Oct 10, 2024 9:01:53 PM dr.app.beast.BeastMain
SEVERE:
Error in input BEAST XML file, 13PCG_amphiclock_3part_BD_noG3rd_SLC_run2.xml: Error parsing '' element with id, 'null':
Incorrect file format, no sample is found !