BEAST v1.8.4, 2002-2016 Bayesian Evolutionary Analysis Sampling Trees Designed and developed by Alexei J. Drummond, Andrew Rambaut and Marc A. Suchard Department of Computer Science University of Auckland 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://beast.bio.ed.ac.uk Source code distributed under the GNU Lesser General Public License: http://github.com/beast-dev/beast-mcmc BEAST developers: Alex Alekseyenko, Guy Baele, Trevor Bedford, Filip Bielejec, Erik Bloomquist, Matthew Hall, 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 Using BEAGLE library v2.1.2 for accelerated, parallel likelihood evaluation 2009-2013, BEAGLE Working Group - http://beagle-lib.googlecode.com/ Citation: Ayres et al (2012) Systematic Biology 61: 170-173 | doi:10.1093/sysbio/syr100 Random number seed: 1494127264712 Parsing XML file: SM_Trt_nDtFR_?Strict_Constant_500ml.xml File encoding: MacRoman Looking for plugins in /Users/DrAlsahafi/Desktop/Alignments_MEGA/BEAST/SM_Trt_noDate_noFR_HKY_Strict_Constant_500ml/plugins Read alignment: alignment Sequences = 32 Sites = 41037 Datatype = nucleotide Site patterns 'patterns' created by merging 2 pattern lists pattern count = 17583 Read attribute patterns, 'Diagns.pattern' for attribute, Diagns Creating the tree model, 'treeModel' initial tree topology = (((((((((00_KK23_DEU,01_SM6_HKG),06_ST6_GBR),01_SA41_ZAF),(02_NN2025_JPN,06_ST1_GBR)),06_W6_GBR),(((01_SM1_HKG,LJ23_RevComp_1),(05_U2A_TUR,06_A19_GBR)),(01_NLML4_GBR,06_M2A_GBR))),(((((01_SF1_USACA,06_T4_GBR),01_AC4446_DEU),01_NLML9_GBR),(01_SF14_USACA,01_SM4_HKG)),(((01_NLML5_GBR,06_U138_GBR),06_G123_GBR),02_NLML8_GBR))),(((06_A9_GBR,UA159_USA),01_NLML1_GBR),06_M21_GBR)),(((01_S1B_TUR,66_GS5),05_U2B_TUR),(01_SA38_ZAF,01_SF12_USACA))) tree height = 2.482461830862473 Using strict molecular clock model. Using strict molecular clock model. Creating state frequencies model 'frequencies': Using empirical frequencies from data = {0.20593, 0.3123, 0.28266, 0.19912} Creating HKY substitution model. Initial kappa = 2.0 Creating site model: with initial relative rate = 1.0 4 category discrete gamma with initial shape = 0.5 Using BEAGLE TreeLikelihood Branch rate model used: strictClockBranchRates Using BEAGLE resource 0: CPU with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU Ignoring ambiguities in tree likelihood. With 17583 unique site patterns. Using rescaling scheme : dynamic (rescaling every 100 evaluations, delay rescaling until first overflow) Creating state frequencies model 'Diagns.frequencies': Initial frequencies = {0.33333, 0.33333, 0.33333} General Substitution Model (stateCount=3) Using BSSVS General Substitution Model Creating site model. Using BEAGLE TreeLikelihood Branch rate model used: strictClockBranchRates Using BEAGLE resource 0: CPU with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU Ignoring ambiguities in tree likelihood. With 1 unique site patterns. Using rescaling scheme : dynamic (rescaling every 100 evaluations, delay rescaling until first overflow) Optimization Schedule: log Constructing a cache around likelihood 'null', signal = Diagns.rates Likelihood computation is using an auto sizing thread pool. Creating the MCMC chain: chainLength=500000000 autoOptimize=true autoOptimize delayed for 5000000 steps WARNING: Likelihood component, null, created but not used in the MCMC Citations for this analysis: FRAMEWORK BEAST primary citation: Drummond AJ, Suchard MA, Xie Dong, Rambaut A (2012) Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol. 29, 1969-1973. DOI:10.1093/molbev/mss075 Using BEAGLE likelihood calculation library: Ayres et al (2012) BEAGLE: a common application programming inferface and high-performance computing library for statistical phylogenetics. Syst Biol. 61, 170-173. DOI:10.1093/sysbio/syr100 SUBSTITUTION MODELS HKY nucleotide substitution model: Hasegowa M, Kishino H, Yano T (1985) Dating the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol.. 22, 160-174 Discrete gamma-distributed rate heterogeneity model: Yang Z (1994) Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol.. 39, 306-314 Stochastic search variable selection, reversible substitution model: Lemey P, Rambaut A, Drummond AJ (2009) Bayesian phylogeography finds its roots. PLoS Computational Biology. e1000520 # BEAST v1.8.4 # Generated Sat May 06 23:23:04 EDT 2017 [seed=1494127264712] # -window -working -options state Posterior Prior Likelihood rootHeight Diagns.nonZeroRates 0 -4025572.5053 -40.6727 -4025531.8326 2.48246 3.00000 - State 85: State was not correctly restored after reject step. Likelihood before: -3962236.6384208333 Likelihood after: -3962245.0901440266 Operator: bitFlip(Diagns.indicators) bitFlip(Diagns.indicators) Details Before: CompoundLikelihood(compoundModel)=( LogNormal(kappa)=-1.8654, Exponential(alpha)=-0.3069, OneOnX(constant.popSize)=-0.0157, Poisson(Diagns.nonZeroRates)=-0.6931, Uniform(Diagns.frequencies)=0.0, CachedDistributionLikelihood(cachedPrior)=-2.3427, CoalescentLikelihood(coalescentLikelihood[coalescent])=-37.034, StrictClockBranchRates(strictClockBranchRates[SM_core_snps_noFR.branchRates])=0.0, StrictClockBranchRates(strictClockBranchRates[Diagns.branchRates])=0.0, SVSGeneralSubstitutionModel-connectedness=0.0 Total = -42.25780916213388 ), CompoundLikelihood(compoundModel)=( BeagleTreeLikelihood(treeLikelihood)=-3962165.0824, AncestralStateBeagleTreeLikelihood(treeLikelihood[Diagns.treeLikelihood])=-29.2983 Total = -3962194.380611671 ) Total = -3962236.638420Underflow calculating likelihood. Attempting a rescaling... 8333 After: CompoundLikelihood(compoundModel)=( LogNormal(kappa)=-1.8654, Exponential(alpha)=-0.3069, OneOnX(constant.popSize)=-0.0157, Poisson(Diagns.nonZeroRates)=-0.6931, Uniform(Diagns.frequencies)=0.0, CachedDistributionLikelihood(cachedPrior)=-2.3427, CoalescentLikelihood(coalescentLikelihood[coalescent])=-37.034, StrictClockBranchRates(strictClockBranchRates[SM_core_snps_noFR.branchRates])=0.0, StrictClockBranchRates(strictClockBranchRates[Diagns.branchRates])=0.0, SVSGeneralSubstitutionModel-connectedness=0.0 Total = -42.25780916213388 ), CompoundLikelihood(compoundModel)=( BeagleTreeLikelihood(treeLikelihood)=-3962165.0824, AncestralStateBeagleTreeLikelihood(treeLikelihood[Diagns.treeLikelihood])=-37.75 Total = -3962202.8323348644 ) Total = -3962245.0901440266 Exception in thread "Thread-7" java.lang.RuntimeException: An error was encounted. Terminating BEAST at dr.util.ErrorLogHandler.publish(Unknown Source) at java.util.logging.Logger.log(Logger.java:509) 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. at java.util.logging.Logger.doLog(Logger.java:531) at java.util.logging.Logger.log(Logger.java:554) at java.util.logging.Logger.severe(Logger.java:1041) at dr.inference.markovchain.MarkovChain.runChain(Unknown Source) at dr.inference.mcmc.MCMC.chain(Unknown Source) at dr.inference.mcmc.MCMC.run(Unknown Source) at java.lang.Thread.run(Thread.java:695) WARNING: Likelihood component, null, created but not used in the MCMC