CladeAge analysis not running

[Philippe Gaubert]

Dear all,

I am encoutering troubles when trying to run an analysis with the CladeAge calibration method. In short, I have delimited CladeAge priors for two clades (one outgroup and one ingroup, which are sister-group), but running BEAST2 ends up with this error message (below).

Any help appreciated,

Philippe.

------------------------------
Updating FossilCalibration FossilCallibration.0
Start likelihood: -Infinity after 10 initialisation attempts
P(posterior) = -Infinity (was -Infinity)
    P(prior) = -22.507359311875582 (was -22.507359311875582)
        P(BirthDeath.t:Mpf) = -1.9236114134009277 (was -1.9236114134009277)
        P(BirthRatePrior.t:Mpf) = -3.404015198231228 (was -3.404015198231228)
        P(RateACPrior.s:Mpf) = -3.184008455701433 (was -3.184008455701433)
        P(RateAGPrior.s:Mpf) = -3.1686658147294304 (was -3.1686658147294304)
        P(RateATPrior.s:Mpf) = -3.184008455701433 (was -3.184008455701433)
        P(RateCGPrior.s:Mpf) = -3.184008455701433 (was -3.184008455701433)
        P(RateGTPrior.s:Mpf) = -3.184008455701433 (was -3.184008455701433)
        P(DeathRatePrior.t:Mpf) = -2.0943972078290636 (was -2.0943972078290636)
        P(ucldStdevPrior.c:Mpf) = 0.819364145120802 (was 0.819364145120802)
    P(likelihood) = -251054.9163381204 (was -251054.9163381204)
        P(treeLikelihood.Mpf) = -251054.91633Fatal exception: Could not find a proper state to initialise. Perhaps try another seed.
81204 (was -251054.9163381204)
    P(fossilCalibrations) = -Infinity (was -Infinity)
        P(F.fossilprior) = -Infinity (was -Infinity)
        P(M.fossilprior) = 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.<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.
-----------------------------------

[michaelm]

Hi Philippe,

could it be that you specified a starting tree that is incompatible with the specified fossil age? So that a clade appears younger in the starting tree than the fossil assigned to it? This could also happen if you used a random starting tree and the clade was younger than the fossil in the 10 random starting trees tested by BEAST2. In that case, specifying a starting tree that is compatible with the fossil age would help.

Let me know if this doesn't fix the issue or if you have other questions.

Cheers,

Michael