I tried to load my sequences after opening the template (contemp) in the BEAUti, but the window became blank and responded nothing.
My beauti version is 2.4.8, and the phylodynamics version is 1.2.1. Some the last messages with the error were:
Failed to load BEAGLE library: no hmsbeagle-jni in java.library.path
TreeLikelihood(treeLikelihood.outbreak_sim0) uses BeerLikelihoodCore4
Alignment(outbreak_sim): [taxa, patterns, sites] = [20, 10000, 10000]
Adding beast.evolution.sitemodel.SiteModel SiteModel.s:outbreak_sim
Adding beast.evolution.likelihood.ThreadedTreeLikelihood treeLikelihood.outbreak_sim
Adding beast.math.distributions.Prior ClockPrior.c:outbreak_sim
Adding beast.math.distributions.Prior MutationRatePrior.s:outbreak_sim
Adding beast.evolution.alignment.TaxonSet TaxonSet.outbreak_sim
Adding beast.evolution.tree.Tree ((((((2:0.00913823207720426,14:0.00913823207720426)20:0.0502941026760681,(6:0.005787716280129395,10:0.005787716280129395)21:0.05364461847314296)22:0.1325052376552091,((7:0.018279534483591313,4:0.018279534483591313)23:0.05469023766567841,16:0.07296977214926972)24:0.11896780025921175)25:0.36631946794955167,8:0.5582570403580331)26:0.1378885021142684,(((11:0.08635200548358422,13:0.08635200548358422)27:0.17975802652227457,(17:0.09797382937468066,12:0.09797382937468066)28:0.16813620263117815)29:0.009694136089329675,(18:0.06720657249130126,(0:0.05603286026672478,19:0.05603286026672478)30:0.011173712224576478)31:0.20859759560388724)32:0.42034137437711305)33:0.09905786193595312,((3:0.36677799503545255,(9:0.05324702569219307,1:0.05324702569219307)34:0.31353096934325947)35:0.26865218527627216,(5:0.18969101821690887,15:0.18969101821690887)36:0.44573916209481584)37:0.15977322409652994)38:0.0
Adding beast.evolution.tree.RandomTree ((((((2:0.00913823207720426,14:0.00913823207720426)20:0.0502941026760681,(6:0.005787716280129395,10:0.005787716280129395)21:0.05364461847314296)22:0.1325052376552091,((7:0.018279534483591313,4:0.018279534483591313)23:0.05469023766567841,16:0.07296977214926972)24:0.11896780025921175)25:0.36631946794955167,8:0.5582570403580331)26:0.1378885021142684,(((11:0.08635200548358422,13:0.08635200548358422)27:0.17975802652227457,(17:0.09797382937468066,12:0.09797382937468066)28:0.16813620263117815)29:0.009694136089329675,(18:0.06720657249130126,(0:0.05603286026672478,19:0.05603286026672478)30:0.011173712224576478)31:0.20859759560388724)32:0.42034137437711305)33:0.09905786193595312,((3:0.36677799503545255,(9:0.05324702569219307,1:0.05324702569219307)34:0.31353096934325947)35:0.26865218527627216,(5:0.18969101821690887,15:0.18969101821690887)36:0.44573916209481584)37:0.15977322409652994)38:0.0
Adding beast.evolution.speciation.YuleModel YuleModel.t:outbreak_sim
Adding beast.evolution.tree.TreeHeightLogger TreeHeight.t:outbreak_sim
Adding beast.core.Logger treelog.t:outbreak_sim
Adding beast.evolution.operators.ScaleOperator ScaleOperator(proportionInvariantScaler.s:outbreak_sim) 0.5000 0 0 NaN
Adding beast.evolution.operators.ScaleOperator ScaleOperator(mutationRateScaler.s:outbreak_sim) 0.5000 0 0 NaN
Adding beast.evolution.operators.ScaleOperator ScaleOperator(gammaShapeScaler.s:outbreak_sim) 0.5000 0 0 NaN
Adding beast.evolution.operators.TipDatesRandomWalker TipDatesRandomWalker(allTipDatesRandomWalker.t:outbreak_sim) 1.0000 0 0 NaN
Adding beast.evolution.operators.ScaleOperator ScaleOperator(YuleModelTreeScaler.t:outbreak_sim) 0.5000 0 0 NaN
Adding beast.evolution.operators.ScaleOperator ScaleOperator(YuleModelTreeRootScaler.t:outbreak_sim) 0.5000 0 0 NaN
Adding beast.evolution.operators.Uniform Uniform(YuleModelUniformOperator.t:outbreak_sim) - 0 0 NaN
Adding beast.evolution.operators.SubtreeSlide SubtreeSlide(YuleModelSubtreeSlide.t:outbreak_sim) 1.0000 0 0 NaN
Adding beast.evolution.operators.Exchange Exchange(YuleModelNarrow.t:outbreak_sim) - 0 0 NaN
Adding beast.evolution.operators.Exchange Exchange(YuleModelWide.t:outbreak_sim) - 0 0 NaN
Adding beast.evolution.operators.WilsonBalding WilsonBalding(YuleModelWilsonBalding.t:outbreak_sim) - 0 0 NaN
Adding beast.math.distributions.Prior YuleBirthRatePrior.t:outbreak_sim
Adding beast.math.distributions.Prior GammaShapePrior.s:outbreak_sim
Adding beast.math.distributions.Prior PropInvariantPrior.s:outbreak_sim
Adding beast.evolution.operators.ScaleOperator ScaleOperator(YuleBirthRateScaler.t:outbreak_sim) 0.7500 0 0 NaN
Adding beast.evolution.operators.ScaleOperator ScaleOperator(StrictClockRateScaler.c:outbreak_sim) 0.7500 0 0 NaN
Adding beast.evolution.operators.UpDownOperator UpDownOperator(strictClockUpDownOperator.c:outbreak_sim) 0.7500 0 0 NaN
BeautiDoc: Could not find object likelihood
BeautiDoc: Could not find object prior
>>> No description for connector YuleModel.t:$(n) == prior
>>> No description for connector ClockPrior.c:$(n) == prior
>>> No description for connector MutationRatePrior.s:$(n) == prior
>>> No description for connector GammaShapePrior.s:$(n) == prior
>>> No description for connector PropInvariantPrior.s:$(n) == prior
>>> No description for connector YuleBirthRatePrior.t:$(n) == prior
InPosterior=posterior prior likelihood
PARTITIONS:
[[], [], []]
PARTITIONS0:
[[], [], []]
PARTITIONS0:
[[], [], []]
PARTITIONS0:
[[], [], []]
PARTITIONS0:
[[], [], []]
Validation message: At least one input of name 'xx' must be specified.
PARTITIONS0:
[[], [], []]
class beast.core.MCMC != class beast.core.Runnable
class beast.core.util.CompoundDistribution != class beast.core.Distribution
I tried to load my sequences after opening the template (contemp) in the BEAUti, but the window became blank and responded nothing.
My beauti version is 2.4.8, and the phylodynamics version is 1.2.1. Some the last messages with the error were:
Could you suggest me some possible solutions?