BEAST v2.1.3, 2002-2014 Bayesian Evolutionary Analysis Sampling Trees Designed and developed by Remco Bouckaert, Alexei J. Drummond, Andrew Rambaut and Marc A. Suchard Department of Computer Science University of Auckland remco@cs.auckland.ac.nz alexei@cs.auckland.ac.nz Institute of Evolutionary Biology University of Edinburgh a.rambaut@ed.ac.uk David Geffen School of Medicine University of California, Los Angeles msuchard@ucla.edu Downloads, Help & Resources: http://beast2.cs.auckland.ac.nz Source code distributed under the GNU Lesser General Public License: http://code.google.com/p/beast2 BEAST developers: Alex Alekseyenko, Trevor Bedford, Erik Bloomquist, 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 File: Tits_HbA-cytb_tree1e7.xml seed: 1483155768598 threads: 1 Random number seed: 1483155768598 Probing: beast.jar Skip loading file:/E:/ProSofts/Phylogeny/BEAST v2.1.3/lib/beast.jar: contains classs beast.app.BEASTVersion that is already loaded Probing: beast.src.jar Loaded URL file:/E:/ProSofts/Phylogeny/BEAST v2.1.3/lib/beast.src.jar Warning: corrupt classpath entry: E:\ProSofts\Phylogeny\BEAST v2.1.3\BEAST.exe Uniform => beast.math.distributions.Uniform Exponential => beast.math.distributions.Exponential LogNormal => beast.math.distributions.LogNormalDistributionModel Normal => beast.math.distributions.Normal Beta => beast.math.distributions.Beta Gamma => beast.math.distributions.Gamma LaplaceDistribution => beast.math.distributions.LaplaceDistribution prior => beast.math.distributions.Prior InverseGamma => beast.math.distributions.InverseGamma OneOnX => beast.math.distributions.OneOnX Element data found with idref='bA_PaAe17_consA'. All other attributes are ignored. Element data found with idref='aA_PaAe17_consA'. All other attributes are ignored. Element data found with idref='Cytb_PaAe17spstre'. All other attributes are ignored. Element tree found with idref='Tree.t:bA_PaAe17_consA'. All other attributes are ignored. Element tree found with idref='Tree.t:aA_PaAe17_consA'. All other attributes are ignored. Element tree found with idref='Tree.t:Cytb_PaAe17spstre'. All other attributes are ignored. Element tree found with idref='Tree.t:bA_PaAe17_consA'. All other attributes are ignored. Element tree found with idref='Tree.t:aA_PaAe17_consA'. All other attributes are ignored. Element tree found with idref='Tree.t:Cytb_PaAe17spstre'. All other attributes are ignored. Element parameter found with idref='clockRate.c:bA_PaAe17_consA'. All other attributes are ignored. Element parameter found with idref='clockRate.c:Cytb_PaAe17spstre'. All other attributes are ignored. Element parameter found with idref='birthRate.t:Species'. All other attributes are ignored. Element parameter found with idref='popMean'. All other attributes are ignored. Element parameter found with idref='popSize'. All other attributes are ignored. Element tree found with idref='Tree.t:Species'. All other attributes are ignored. Element tree found with idref='Tree.t:bA_PaAe17_consA'. All other attributes are ignored. Element tree found with idref='Tree.t:aA_PaAe17_consA'. All other attributes are ignored. Element tree found with idref='Tree.t:Cytb_PaAe17spstre'. All other attributes are ignored. Element parameter found with idref='popSizeTop'. All other attributes are ignored. Element parameter found with idref='clockRate.c:bA_PaAe17_consA'. All other attributes are ignored. Element tree found with idref='Tree.t:bA_PaAe17_consA'. All other attributes are ignored. Element parameter found with idref='clockRate.c:Cytb_PaAe17spstre'. All other attributes are ignored. Element tree found with idref='Tree.t:Cytb_PaAe17spstre'. All other attributes are ignored. Element parameter found with idref='clockRate.c:Cytb_PaAe17spstre'. All other attributes are ignored. Element tree found with idref='Tree.t:Cytb_PaAe17spstre'. All other attributes are ignored. Element parameter found with idref='clockRate.c:bA_PaAe17_consA'. All other attributes are ignored. Element tree found with idref='Tree.t:bA_PaAe17_consA'. All other attributes are ignored. Element parameter found with idref='clockRate.c:bA_PaAe17_consA'. All other attributes are ignored. Element parameter found with idref='clockRate.c:Cytb_PaAe17spstre'. All other attributes are ignored. Element parameter found with idref='mutationRate.s:aA_PaAe17_consA'. All other attributes are ignored. Element parameter found with idref='mutationRate.s:bA_PaAe17_consA'. All other attributes are ignored. Element parameter found with idref='mutationRate.s:Cytb_PaAe17spstre'. All other attributes are ignored. Element parameter found with idref='birthRate.t:Species'. All other attributes are ignored. Ae_bonvaloti: 1436 4 Ae_fuliginosus: 1436 4 Ae_caudatus: 1436 4 Ae_concinnus: 1436 4 Sy_modestus: 1436 4 Cy_cyanus: 1436 4 Pa_humilis: 1436 4 Pa_m_tibetanus: 1436 4 Pa_m_minor: 1436 4 Pa_monticolus: 1436 4 Pa_spilonotus: 1436 4 Pe_a_aemodius: 1436 4 Pe_a_pekinensis: 1436 4 Pe_rubidiventris: 1436 4 Pe_venustulus: 1436 4 Lo_d_dichroides_L: 1436 4 Po_m_baicalensis: 1436 4 Po_p_hypermelaenus: 1436 4 Po_p_brevirostris: 1436 4 Po_davidi: 1436 4 Pa_spilonotus: 675 4 Pa_monticolus: 675 4 Pa_humilis: 675 4 Cy_cyanus: 675 4 Pa_m_tibetanus: 675 4 Pa_m_minor: 675 4 Lo_d_dichroides_L: 675 4 Pe_venustulus: 675 4 Pe_rubidiventris: 675 4 Pe_a_pekinensis: 675 4 Pe_a_aemodius: 675 4 Pe_a_aemodius_2: 675 4 Po_p_hypermelaenus: 675 4 Po_p_brevirostris: 675 4 Po_m_baicalensis: 675 4 Po_m_weigoldicus: 675 4 Po_davidi: 675 4 Ae_fuliginosus: 675 4 Ae_concinnus: 675 4 Ae_caudatus: 675 4 Ae_bonvaloti: 675 4 Sy_modestus: 675 4 Ae_bonvaloti: 1045 4 Ae_caudatus: 1045 4 Ae_concinnus: 1045 4 Ae_f20 taxa 1436 sites 309 patterns 22 taxa 675 sites 92 patterns uliginosus: 1045 4 Cy_cyanus: 1045 4 Lo_d_dichroides: 1045 4 Pa_humilis: 1045 4 Pa_m_minor: 1045 4 Pa_m_tibetanus: 1045 4 Pa_monticolus: 1045 4 Pa_spilonotus: 1045 4 Pe_rubidiventris: 1045 4 Pe_a_aemodius: 1045 4 Pe_a_pekinensis: 1045 4 Pe_venustulus: 1045 4 Po_davidi: 1045 4 Po_m_baicalensis: 1045 4 Po_m_weigoldicus: 1045 4 Po_p_brevirostris: 1045 4 Po_p_hypermelaenus: 1045 4 Sy_modestus: 1045 4 Starting frequencies: [0.1660340129623913, 0.3783231231458531, 0.23933485514012207, 0.21630800875163006] Failed to load BEAGLE library: no hmsbeagle-jni in java.library.path Starting frequencies: [0.22281055660395982, 0.26347001175316337, 0.3378665207386376, 0.17585291090428173] Failed to load BEAGLE library: no hmsbeagle-jni in java.library.path Starting frequencies: [0.2711554147459938, 0.3602223227714642, 0.12844079724821836, 0.2401814652343272] Failed to load BEAGLE library: no hmsbeagle-jni in java.library.path 21 taxa 1045 sites 357 patterns TreeLikelihood uses beast.evolution.likelihood.BeerLikelihoodCore4 TreeLikelihood uses beast.evolution.likelihood.BeerLikelihoodCore4 TreeLikelihood uses beast.evolution.likelihood.BeerLikelihoodCore4 ====================================================== Please cite the following when publishing this model: Remco Bouckaert, Joseph Heled, Denise Kuehnert, Tim Vaughan, Chieh-Hsi Wu, Dong Xie, Marc Suchard, Andrew Rambaut, Alexei J Drummond BEAST 2: A software platform for Bayesian evolutionary analysis. PLOS Computational Biology 10(4): e1003537, 2014 Hasegawa, M., Kishino, H and Yano, T. 1985. Dating the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution 22:160-174. ====================================================== Start likelihood: NaN P(posterior) = NaN (was NaN) P(speciescoalescent) = NaN (was NaN) P(SpeciesTreePopSize.Species) = NaN (was NaN) P(treePrior.t:Cytb_PaAe17spstre) = NaN (was NaN) P(treePrior.t:aA_PaAe17_consA) = NaN (was NaN) P(treePrior.t:bA_PaAe17_consA) = NaN (was NaN) P(prior) = NaN (was NaN) P(YuleModel.t:Species) = NaN (was NaN) P(YuleBirthRatePrior.t:Species) = -5.362240542149371 (was NaN) P(ClockPrior.c:Cytb_PaAe17spstre) = -1.4620820845188824 (was NaN) P(ClockPrior.c:bA_PaAe17_consA) = -1.4620820845188824 (was NaN) P(MutationRatePrior.s:Cytb_PaAe17spstre) = -1.4620820845188824 (was NaN) P(MutationRatePrior.s:aA_PaAe17_consA) = -1.8862943611198906 (was NaN) P(MutationRatePrior.s:bA_PaAe17_consA) = -1.8862943611198906 (was NaN) P(popMean.prior) = 0.0 (was NaN) P(likelihood) = NaN (was NaN) P(treeLikelihood.aA_PaAe17_consA) = NaN (was NaN) P(treeLikelihood.bA_PaAe17_consA) = NaN (was NaN) P(treeLikelihood.Cytb_PaAe17spstre) = NaN (was NaN) java.lang.Exception: Could not find a proper state to initialise. Perhaps try another seed. at beast.core.MCMC.run(Unknown Source) at beast.app.BeastMCMC.run(Unknown Source) at beast.app.beastapp.BeastMain.(Unknown Source) at beast.app.beastapp.BeastMain.main(Unknown Source)