problems building the xml file for Star Beast

[Manuel Pimentel]

Dear all,

I have encountered a problem building the xml file with Beauti. I have included two alignments (plastid and nuclear) each of them with 205 specimens (equal specimens in both alignments) corresponding to 14 species (taxon assignment was done by Beauti using sample names). When I try to run the file in Beast I receive this answer:


Start likelihood: -Infinity after 11 initialisation attempts
P(posterior) = -Infinity (was NaN)
    P(speciescoalescent) = -1631.397690192408 (was NaN)
        P(SpeciesTreePopSize.Species) = 79.60913942800259 (was NaN)
        P(treePrior.t:Concat_plastid_121114) = -659.1679390478646 (was NaN)
        P(treePrior.t:nuclear_final_111114) = -1051.838890572546 (was NaN)
    P(prior) = -Infinity (was NaN)
        P(YuleModel.t:Species) = 23.085120070943667 (was NaN)
        P(YuleBirthRatePrior.t:Species) = -2.4768316425445907 (was NaN)
        P(ClockPrior.c:nuclear_final_111114) = NaN (was NaN)
        P(GammaShapePrior.s:Concat_plastid_121114) = -1.0 (was NaN)
        P(GammaShapePrior.s:nuclear_final_111114) = -1.0 (was NaN)
        P(popMean.prior) = 0.0 (was NaN)
        P(RateACPrior.s:Concat_plastid_121114) = -3.184008455701433 (was NaN)
        P(RateACPrior.s:nuclear_final_111114) = -3.184008455701433 (was NaN)
        P(RateAGPrior.s:Concat_plastid_121114) = -3.1686658147294304 (was NaN)
        P(RateAGPrior.s:nuclear_final_111114) = -3.1686658147294304 (was NaN)
        P(RateATPrior.s:Concat_plastid_121114) = -3.184008455701433 (was NaN)
        P(RateATPrior.s:nuclear_final_111114) = -3.184008455701433 (was NaN)
        P(RateCGPrior.s:Concat_plastid_121114) = -3.184008455701433 (was NaN)
        P(RateCGPrior.s:nuclear_final_111114) = -3.184008455701433 (was NaN)
        P(RateGTPrior.s:Concat_plastid_121114) = -3.184008455701433 (was NaN)
        P(RateGTPrior.s:nuclear_final_111114) = -3.184008455701433 (was NaN)
        P(Meliceae.prior) = NaN (was NaN)
    P(likelihood) = NaN (was NaN)
        P(treeLikelihood.Concat_plastid_121114) = NaN (was NaN)
        P(treeLikelihood.nuclear_final_111114) = NaN (was NaN)
java.lang.Exception: 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)
 
I have checked previous messages in the group and I saw that a similar problem was discussed. In that occasion Remco suggested that increasing the upper limit in:

<parameter id="birthRate.t:Species" lower="0.0" name="stateNode" upper="1e10">213.2021</parameter>

could solve the problem. I tried (up to 1e45) but the result is the same.

I would be very grateful if someone could help me with this problem. Sorry if the answer is too obvious, I am completely lost right now.

All best

Manuel