Taxon set specifying distribution but an error encountered

[bioz...@gmail.com]

Dear all

 

In BEAUti 2.1.3, I used Taxon set editor to specify some taxon sub-group, and I noticed there is a prior specifying option by which we can choose a distribution for a taxon sub-group.

But I am wonderring the exact meaning of this proior distribution, can anyone tell me?

 

However,  if I chose one distribution(e.g. gamma), the analysis running would be terminated with the error prompt as follows:

 

NaN (was NaN)
  P(treeLikelihood.CA6CLADE20122013) = NaN (was NaN)
  P(locationtreeLikelihood.LATLONG) = 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)

 

Can anyone help me address this issue?

 

Thanks very much!

 

Jie

[Remco Bouckaert]

Dear Jie,

Can you have a look at the complete error message, including all numbers for the prior? If something goes wrong with the prior (say, resulting in an infinite log prior), the posterior is not calculated, but BEAST stops immediately. The numbers for the posterior are still reported as NaNs, just like the way you posted, but the problem is probably somewhere with one of the priors.

Cheers,

Remco

[bioz...@gmail.com]

Dear Doctor

 

I found if I had separately chosen the normal distribution, uniform distribution and the laplace distribution for my taxon set, the run would be ok, but if I had chosen other distributions, then the errors would occur. Moreover, I found there were two types of error prompt and I have attached them in the attachment for you check, and hope they are helpful for you to help me address my issues.  

 

However, I am still wonderring about the exact meanings of these proior distributions, can anyone tell me something about them?

 

Thanks very much!

 

Cheers,

 

Jie
在 2014年11月3日星期一UTC+8上午3时53分36秒，Remco Bouckaert写道：

[bioz...@gmail.com]

Dear doctor

 

I have another wandering about how to use BEAST 2.1.3:

 

I am trying to conduct a phylogeography analysis using  BEAUti 2.1.3 to set up some input options.  After I finished importing sequences datas and the respective latitude&longitude datas in to BEAUti, however, I could not find the respective diffusion model options used in BEAUti 1.8.0 under the site model tab e.g. "homognous Browin diffusion model",  (I have unlink the site model), but by contrast, the respective diffusion models I found  were actually the nucleotide substitution models e.g. JC69.

 

Can anyone tell me why I can not find the respective diffusion model?

 

Thanks very much!

 

Jie

在 2014年11月3日星期一UTC+8上午3时53分36秒，Remco Bouckaert写道：

Dear Jie,