Could not find a proper state to initialise error

[Junxia Zhang]

Hello all,

I am trying to run BEAST analysis on a dataset with 300 taxa and 25 genes (all concatenated and treated as one partition) using BEAST v.2.4.5, but always get following error message. This analysis is attempted on a fixed tree topology to reduce the computational time. Can anyone help me to figure out what is wrong with this analysis? (the xml file for the analysis is attached here in case it is useful for troubleshooting.)

Thanks a lot!

Junxia

Random number seed: 1506724860891

Alignment(T300)

  300 taxa

  13787 sites

  10811 patterns

  UCRelaxedClockModel: using 598 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

Drummond AJ, Ho SYW, Phillips MJ, Rambaut A (2006) Relaxed Phylogenetics and

  Dating with Confidence. PLoS Biol 4(5): e88

===============================================================================

Start likelihood: -Infinity after 100 initialisation attempts

P(posterior) = -Infinity (was -Infinity)

P(prior) = -12481.063813949075 (was -12481.063813949075)

P(YuleModel.t:T300) = -12401.244800000015 (was -12401.244800000015)

P(YuleBirthRatePrior.t:T300) = -1.8862943611198906 (was -1.8862943611198906)

P(GammaShapePrior.s:T300) = -1.0 (was -1.0)

P(RateACPrior.s:T300) = -3.184008455701433 (was -3.184008455701433)

P(RateAGPrior.s:T300) = -3.1686658147294304 (was -3.1686658147294304)

P(RateATPrior.s:T300) = -3.184008455701433 (was -3.184008455701433)

P(RateCGPrior.s:T300) = -3.184008455701433 (was -3.184008455701433)

P(RateGTPrior.s:T300) = -3.184008455701433 (was -3.184008455701433)

P(MeanRatePrior.c:T300) = 0.0 (was 0.0)

P(ucldStdevPrior.c:T300) = 0.819364145120802 (was 0.819364145120802)

P(Con1.prior) = -4.740574822994295 (was -4.740574822994295)

P(Con10.prior) = -5.071416766356115 (was -5.071416766356115)

P(Con11.prior) = -5.269403356383394 (was -5.269403356383394)

P(Con12.prior) = -5.269403356383394 (was -5.269403356383394)

P(Con14.prioFatal exception: Could not find a proper state to initialise. Perhaps try another seed.

r) = -5.159629846774143 (was -5.159629846774143)

P(Con17.prior) = -5.159629846774143 (was -5.159629846774143)

P(Con18.prior) = -5.159629846774143 (was -5.159629846774143)

P(Con3.prior) = -5.269403356383394 (was -5.269403356383394)

P(Con4.prior) = -5.269403356383394 (was -5.269403356383394)

P(Con5.prior) = -5.159629846774143 (was -5.159629846774143)

P(Con8.prior) = -5.159629846774143 (was -5.159629846774143)

P(Con9.prior) = -5.159629846774143 (was -5.159629846774143)

P(likelihood) = -Infinity (was -Infinity)

P(treeLikelihood.T300) = -Infinity (was -Infinity)

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.<init>(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.

BEAST has terminated with an error. Please select QUIT from the menu.