BEAST v2.4.5, 2002-2016 Bayesian Evolutionary Analysis Sampling Trees Designed and developed by Remco Bouckaert, Alexei J. Drummond, Andrew Rambaut & 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.org/ Source code distributed under the GNU Lesser General Public License: http://github.com/CompEvol/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 Random number seed: 1490514091910 Alignment(ITS_3M) 174 taxa 551 sites 267 patterns Alignment(RPB1_3M) 174 taxa 534 sites 227 patterns Alignment(MCM7_3M1) 174 taxa 439 sites 202 patterns UCRelaxedClockModel: using 346 rate categories to approximate rate distribution across branches. Using BEAGLE version: 2.1.2 resource 0: CPU with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU UCRelaxedClockModel: using 346 rate categories to approximate rate distribution across branches. Using BEAGLE version: 2.1.2 resource 0: CPU with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU UCRelaxedClockModel: using 346 rate categories to approximate rate distribution across branches. Using BEAGLE version: 2.1.2 resource 0: CPU with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU =============================================================================== Citations for this model: Bouckaert RR, Heled J, Kuehnert D, Vaughan TG, Wu C-H, Xie D, Suchard MA, Rambaut A, Drummond AJ (2014) BEAST 2: A software platform for Bayesian evolutionary analysis. PLoS Computational Biology 10(4): e1003537 Graham Jones (2016). Algorithmic improvements to species delimitation and phylogeny estimation under the multispecies coalescent. Journal of Mathematical Biology. DOI 10.1007/s00285-016-1034-0 http://link.springer.com/article/10.1007/s00285-016-1034-0 Jones GR, Aydin Z, and Oxelman B (2015). DISSECT: an assignment-free Bayesian discovery method for species delimitation under the multispecies coalescent. Bioinformatics 31 (7) 991-998. DOI 10.1101/003178 http://bioinformatics.oxfordjournals.org/content/31/7/991. Drummond AJ, Ho SYW, Phillips MJ, Rambaut A (2006) Relaxed Phylogenetics and Dating with Confidence. PLoS Biol 4(5): e88 =============================================================================== P(posterior) = -Infinity (was -Infinity) P(smcCoalescent) = 703.9708568766605 (was 703.9708568766605) P(prior) = -Infinity (was -Infinity) P(BirthDeathCollapseModel.t:Species) = 770.8271685205639 (was 770.8271685205639) P(bdcGrowthRatePrior.t:Species) = -Infinity (was -Infinity) P(bdcCollapseWeight.smcTreePrior) = -Infinity (was -Infinity) P(GammaShapePrior.s:ITS_3M) = -0.39999999999999997 (was -0.39999999999999997) P(GammaShapePrior.s:MCM7_3M1) = -1.0 (was -1.0) P(GammaShapePrior.s:RPB1_3M) = -0.39999999999999997 (was -0.39999999999999997) P(popScalePrior) = -8.849681069015068 (was -8.849681069015068) P(RateACPrior.s:ITS_3M) = -1.4620820845188824 (was -1.4620820845188824) P(RateACPrior.s:MCM7_3M1) = -1.4620820845188824 (was -1.4620820845188824) P(RateACPrior.s:RPB1_3M) = -1.4620820845188824 (was -1.4620820845188824) P(RateAGPrior.s:ITS_3M) = -1.4620820845188824 (was -1.4620820845188824) P(RateAGPrior.s:MCM7_3M1) = -1.4620820845188824 (was -1.4620820845188824) P(RateAGPrior.s:RPB1_Start likelihood: -Infinity after 10 initialisation attempts 3M) = -1.4620820845188824 (was -1.4620820845188824) P(RateATPrior.s:ITS_3M) = -1.4620820845188824 (was -1.4620820845188824) P(RateATPrior.s:MCM7_3M1) = -1.4620820845188824 (was -1.4620820845188824) P(RateATPrior.s:RPB1_3M) = -1.4620820845188824 (was -1.4620820845188824) P(RateCGPrior.s:ITS_3M) = -1.4620820845188824 (was -1.4620820845188824) P(RateCGPrior.s:MCM7_3M1) = -1.4620820845188824 (was -1.4620820845188824) P(RateCGPrior.s:RPB1_3M) = -1.4620820845188824 (was -1.4620820845188824) P(RateCTPrior.s:ITS_3M) = -1.4620820845188824 (was -1.4620820845188824) P(RateCTPrior.s:MCM7_3M1) = -1.4620820845188824 (was -1.4620820845188824) P(RateCTPrior.s:RPB1_3M) = -1.4620820845188824 (was -1.4620820845188824) P(RateGTPrior.s:RPB1_3M) = -1.4620820845188824 (was -1.4620820845188824) P(bdcRelativeDeathRate.smcTreePrior) = -Infinity (was -Infinity) P(UCMeanRatePrior.c:MCM7_3M1) = -1.0 (was -1.0) P(UCMeanRatePrior.c:RPB1_3M) = -1.0 (was -1.0) P(likelihood) = NaN (was NaN) ** P(treeLikelihood.ITS_3M) = NaN (was NaN) ** P(treeLikelihood.RPB1_3M) = NaN (was NaN) ** P(treeLikelihood.MCM7_3M1) = NaN (was NaN) ** java.lang.RuntimeException: 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) at beast.app.beastapp.BeastLauncher.main(Unknown Source) Fatal exception: Could not find a proper state to initialise. Perhaps try another seed. Fatal exception: Could not find a proper state to initialise. Perhaps try another seed. BEAST has terminated with an error. Please select QUIT from the menu.