I run the file attached below came accross an error promption as bellow:
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: S_HCOV19_SG-thorney.xml
File encoding: UTF8
Looking for plugins in /usr/local/BEASTv1.10.5pre_thorney_0.1.1/bin/plugins
Using node heights.
Creating the constrained tree model based on big fast tree model, 'treeModel'
taxon count = 1309
tree height = 2.9180651027763442
The gmrfSkyrideLikelihood has time aware smoothing
Creating a GMRF smoothed skyride model for multiple loci (SkyGrid)
Population sizes: 166
Optimization Schedule: default
Likelihood computation is using an auto sizing thread pool.
Creating the MCMC chain:
chain length = 10000000000
operator adaption = true
adaptation delayed for 100000000 steps
Feb 17, 2023 5:50:16 PM dr.app.beast.BeastMain
SEVERE: Error running file: S_HCOV19_SG-thorney.xml
Feb 17, 2023 5:50:16 PM 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)=(
Gamma(clock.rate)=0.2742,
Gamma(skygrid.precision)=-4.6139,
GMRFSkygridLikelihood(gmrfSkyrideLikelihood[skygrid])=-8458.9409
Total = -8463.280662719842
),
CompoundLikelihood(compoundModel)=(
ThorneyTreeLikelihood(thorneyTreeLikelihood[treeLikelihood])=-Inf
Total = -Infinity
)
Total = -Infinity
Dear @jtmccr1
I run the file attached below came accross an error promption as bellow: 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: S_HCOV19_SG-thorney.xml File encoding: UTF8 Looking for plugins in /usr/local/BEASTv1.10.5pre_thorney_0.1.1/bin/plugins Using node heights.
Creating the constrained tree model based on big fast tree model, 'treeModel' taxon count = 1309 tree height = 2.9180651027763442 The gmrfSkyrideLikelihood has time aware smoothing Creating a GMRF smoothed skyride model for multiple loci (SkyGrid) Population sizes: 166 Optimization Schedule: default
Likelihood computation is using an auto sizing thread pool.
Creating the MCMC chain: chain length = 10000000000 operator adaption = true adaptation delayed for 100000000 steps Feb 17, 2023 5:50:16 PM dr.app.beast.BeastMain
SEVERE: Error running file: S_HCOV19_SG-thorney.xml
Feb 17, 2023 5:50:16 PM 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)=( Gamma(clock.rate)=0.2742, Gamma(skygrid.precision)=-4.6139, GMRFSkygridLikelihood(gmrfSkyrideLikelihood[skygrid])=-8458.9409 Total = -8463.280662719842 ), CompoundLikelihood(compoundModel)=( ThorneyTreeLikelihood(thorneyTreeLikelihood[treeLikelihood])=-Inf Total = -Infinity ) Total = -Infinity
S_HCOV19_SG-thorney.zip Best,
Jie