Error: Could not find a proper state to initialise. Perhaps try another seed.

[Tatiana Barroca]

Hi Beast 2.4.3 users 
I generated a xml file and tried to run it with Beast 2.4.3. 
However I am getting this message: 

Alignment(jau_46)

  46 taxa

  794199 sites

  63282 patterns

TreeLikelihood(treeLikelihood.jau_46) uses BeerLikelihoodCore4

  Alignment(jau_46): [taxa, patterns, sites] = [46, 63282, 794199]

Failed to load BEAGLE library: no hmsbeagle-jni in java.library.path

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

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

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

P(posterior) = NaN (was NaN)  **

P(speciescoalescent) = NaN (was NaN)  **

P(SpeciesTreePopSize.Species) = NaN (was NaN)  **

P(treePrior.t:jau_46) = NaN (was NaN)  **

P(prior) = NaN (was NaN)  **

P(CoalescentConstant.t:Species) = 0.0 (was 0.0)

P(popMean.prior) = 0.0 (was 0.0)

P(PopSizePrior.t:Species) = 1.2039728043259361 (was 1.2039728043259361)

P(RateACPrior.s:jau_46) = -3.184008455701433 (was -3.184008455701433)

P(RateAGPrior.s:jau_46) = -3.1686658147294304 (was -3.1686658147294304)

P(RateATPrior.s:jau_46) = -3.184008455701433 (was -3.184008455701433)

P(RateCGPrior.s:jau_46) = -3.184008455701433 (was -3.184008455701433)

P(RateGTPrior.s:jau_46) = -3.184008455701433 (was -3.184008455701433)

P(likelihood) = NaN (was NaN)  **

P(treeLikelihood.jau_46) = 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.<iniStart likelihood: NaN 

Fatal exception: Could not find a proper state to initialise. Perhaps try another seed.

t>(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.

Could anyone help me with this? I think that I have some mistakes in my time units, as it does not find a proper state to initialize:

https://drive.google.com/file/d/0B_XVjJRt8Kw2d0k2a2JXRFQzVVk/view?usp=sharing

Thanks :)

Tatiana

[Remco Bouckaert]

Hi Tatiana, 

Perhaps the starting value for the population size cures the species coalescent to run into numeric problems. If so, trying other starting values might get things going.

If that does not help, perhaps you can send the XML so I can investigate.

Cheers,

Remco

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[Remco Bouckaert]

Hi Tatiana,

Thanks for the file. It turns out that the analysis was set up as StarBeast analysis, but that only a single taxon was specified for the species tree. To fix this, simply specify the taxon sets for the species in the taxonset panel in BEAUti. Or, if you did not want to use a *BEAST analysis, set up the analysis with the Standard template (using the menu File/Templates/Standard in BEAUti).

BEAST should have warned about this with a message saying:

NodeReheight operator requires at least 2 taxa while the taxon set (id=taxonsuperset) has only 1 taxa. If the XML file was set up in BEAUti, this probably means a taxon assignment needs to be set up in the taxonset panel.

but that did not came out in the message you posted, so I will look into what is going wrong.

Cheers,

Remco

[Tatiana Barroca]

Hi Remco,

Thanks again for helping me. Yes, I set up the analysis for StarBeast and I have only a single taxon... Can I run it with only one taxon? I've thought so.

BEAST didn't warned me with the message you wrote. That's why I didn't mention before...

Hope to hear from you soon!

Cheers:)

Tatiana

[Remco Bouckaert]

Hi Tatiana,

A *BEAST analysis is usually done to infer species trees, and if there is only one species the tree is already known. Though it is theoretically possible to do a 1 species *BEAST analysis, the tree prior assumes there are at least two species.

Probably the closest alternative is to run a Standard analysis with a coalescent based tree prior — the coalescent with constant population would give results close to a *BEAST analysis with constant population (as well as linear with constant root).

Cheers,

Remco

[Tatiana Barroca]

Hi Remco!

I see...So I`ll try this way and let you know if it works.

Thanks!

Cheers:)

Tatiana

Dr. Tatiana Barroca
Population and Conservation Genetics

(31) 3409-2917 (31) 98814-2008

CRBio - 70149/04-D
CT Peixes/UFMG

Currículo Lattes: http://lattes.cnpq.br/4397056059310851

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