An issue about beastlabs.evolution.likelihood.AncestralStateLogger
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Qi Feng
Sep 15, 2025, 2:17:18 PM (10 days ago) Sep 15
to beast-users
Hi,
I am trying to investigate the state distributions of each site in the genetic sequences, for the interested internal node of the phylogenitic tree, during the MCMC samples. When the interested internal node being the root of the tree, I have successflly obtained the states distributions. But when the interested internal node becoming the root of a branch of the tree, an error message occured as below:
java.lang.RuntimeException: Gamma rate heterogeneity or proportion invariant is not supported yet
at beastlabs.evolution.likelihood.AncestralStateLogger.sample(Unknown Source)
at beastlabs.evolution.likelihood.AncestralStateLogger.log(Unknown Source)
at beast.base.inference.Logger.log(Unknown Source)
at beast.base.inference.MCMC.log(Unknown Source)
at beast.base.inference.MCMC.propagateState(Unknown Source)
at beast.base.inference.MCMC.doLoop(Unknown Source)
at beast.base.inference.MCMC.run(Unknown Source)
at beastfx.app.beast.BeastMCMC.run(Unknown Source)
at beastfx.app.beast.Controller$2.run(Unknown Source)
java.lang.RuntimeException: Gamma rate heterogeneity or proportion invariant is not supported yet
at beastlabs.evolution.likelihood.AncestralStateLogger.sample(Unknown Source)
at beastlabs.evolution.likelihood.AncestralStateLogger.log(Unknown Source)
at beast.base.inference.Logger.log(Unknown Source)
at beast.base.inference.MCMC.log(Unknown Source)
at beast.base.inference.MCMC.propagateState(Unknown Source)
at beast.base.inference.MCMC.doLoop(Unknown Source)
at beast.base.inference.MCMC.run(Unknown Source)
at beastfx.app.beast.BeastMCMC.run(Unknown Source)
at beastfx.app.beast.Controller$2.run(Unknown Source)
I attached the succesful and failure xml file for you check the source of the error.
I am trying to investigate the state distributions of each site in the genetic sequences, for the interested internal node of the phylogenitic tree, during the MCMC samples. When the interested internal node being the root of the tree, I have successflly obtained the states distributions. But when the interested internal node becoming the root of a branch of the tree, an error message occured as below:
java.lang.RuntimeException: Gamma rate heterogeneity or proportion invariant is not supported yet
at beastlabs.evolution.likelihood.AncestralStateLogger.sample(Unknown Source)
at beastlabs.evolution.likelihood.AncestralStateLogger.log(Unknown Source)
at beast.base.inference.Logger.log(Unknown Source)
at beast.base.inference.MCMC.log(Unknown Source)
at beast.base.inference.MCMC.propagateState(Unknown Source)
at beast.base.inference.MCMC.doLoop(Unknown Source)
at beast.base.inference.MCMC.run(Unknown Source)
at beastfx.app.beast.BeastMCMC.run(Unknown Source)
at beastfx.app.beast.Controller$2.run(Unknown Source)
java.lang.RuntimeException: Gamma rate heterogeneity or proportion invariant is not supported yet
at beastlabs.evolution.likelihood.AncestralStateLogger.sample(Unknown Source)
at beastlabs.evolution.likelihood.AncestralStateLogger.log(Unknown Source)
at beast.base.inference.Logger.log(Unknown Source)
at beast.base.inference.MCMC.log(Unknown Source)
at beast.base.inference.MCMC.propagateState(Unknown Source)
at beast.base.inference.MCMC.doLoop(Unknown Source)
at beast.base.inference.MCMC.run(Unknown Source)
at beastfx.app.beast.BeastMCMC.run(Unknown Source)
at beastfx.app.beast.Controller$2.run(Unknown Source)
I attached the succesful and failure xml file for you check the source of the error.
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