I am getting the following error when I run the example file rootprobs_phydyn.xml, replicated with BEAST 2.5.0 in Mac and 2.5.2 in Linux. In both cases I am using the latest version of PhyDyn installed using BEAST2's packagemanager.
` Random number seed: 1554775524030
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
Volz EM, Siveroni I. 2018. Bayesian phylodynamic inference with complex models.
PLos Computational Biology. 14(11), ISSN:1553-7358
===============================================================================
Start likelihood: -147.55053790038968
Writing file rootStateProbabilities_phydyn.log
Trying to write file rootStateProbabilities_phydyn.log but the file already exists (perhaps use the -overwrite flag?).
Overwrite (Y/N)?:
Y
Writing file rootStateProbabilities_phydyn.log
Sample posterior
Fatal exception: 11
java.lang.ArrayIndexOutOfBoundsException: 11
at phydyn.distribution.StateProbabilitiesVectors.getRootProbs(Unknown Source)
at phydyn.loggers.STreeRootLogger.log(Unknown Source)
at beast.core.Loggable.log(Unknown Source)
at beast.core.Logger.log(Unknown Source)
at beast.core.MCMC.log(Unknown Source)
at beast.core.MCMC.propagateState(Unknown Source)
at beast.core.MCMC.doLoop(Unknown Source)
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)
Fatal exception: 11
java.lang.RuntimeException: An error was encounted. Terminating BEAST
at beast.app.util.ErrorLogHandler.publish(Unknown Source)
at java.util.logging.Logger.log(Logger.java:738)
at java.util.logging.Logger.doLog(Logger.java:765)
at java.util.logging.Logger.log(Logger.java:788)
at java.util.logging.Logger.severe(Logger.java:1464)
at beast.app.beastapp.BeastMain.(Unknown Source)
at beast.app.beastapp.BeastMain.main(Unknown Source) `
igococha
commented
4 years ago
I am getting the following error when I run the example file rootprobs_phydyn.xml, replicated with BEAST 2.5.0 in Mac and 2.5.2 in Linux. In both cases I am using the latest version of PhyDyn installed using BEAST2's packagemanager. ` Random number seed: 1554775524030
File: rootprobs_phydyn.xml seed: 1554775524030 threads: 1 inv3loc_0: 2 4 inv4loc_1: 2 4 inv5loc_1: 2 4 inv6loc_1: 2 4 inv2loc_0: 2 4 inv1loc_0: 2 4 Alignment(sequences) 6 taxa 2 sites 1 patterns
Warning: Unknown variable name IX in population parameters object model-name = simplemodel; definitions = { gamma01 = m10I1/I0; gamma10 = m01I0/I1; } equations = { F(I0,I0) = 100I0/2; F(I1,I1) = 100I1/2; G(I0,I1) = gamma01I0; G(I1,I0) = gamma10I1; D(I0) = 100I0/2-gamma01I0+gamma10I1; D(I1) = 100I1/2-gamma10I1+gamma01I0; dot(S) = 0; } model-parameters = { m10 = 0.01; dummy = 5.0; m01 = 0.001; } trajectory-parameters = { t0 = -0.1 method=classicrk; integrationSteps=1001; initial-vales = { I0 = 50.0; I1 = 25.0; S = 100.0; }; }
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
Volz EM, Siveroni I. 2018. Bayesian phylodynamic inference with complex models. PLos Computational Biology. 14(11), ISSN:1553-7358
=============================================================================== Start likelihood: -147.55053790038968 Writing file rootStateProbabilities_phydyn.log Trying to write file rootStateProbabilities_phydyn.log but the file already exists (perhaps use the -overwrite flag?). Overwrite (Y/N)?: Y Writing file rootStateProbabilities_phydyn.log Sample posterior Fatal exception: 11 java.lang.ArrayIndexOutOfBoundsException: 11 at phydyn.distribution.StateProbabilitiesVectors.getRootProbs(Unknown Source) at phydyn.loggers.STreeRootLogger.log(Unknown Source) at beast.core.Loggable.log(Unknown Source) at beast.core.Logger.log(Unknown Source) at beast.core.MCMC.log(Unknown Source) at beast.core.MCMC.propagateState(Unknown Source) at beast.core.MCMC.doLoop(Unknown Source) 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)
Fatal exception: 11
java.lang.RuntimeException: An error was encounted. Terminating BEAST
at beast.app.util.ErrorLogHandler.publish(Unknown Source)
at java.util.logging.Logger.log(Logger.java:738)
at java.util.logging.Logger.doLog(Logger.java:765)
at java.util.logging.Logger.log(Logger.java:788)
at java.util.logging.Logger.severe(Logger.java:1464)
at beast.app.beastapp.BeastMain.(Unknown Source)
at beast.app.beastapp.BeastMain.main(Unknown Source) `