tree likelihood NaN

[Pascale Lubbe]

Hi all!

I am trying to set up a relatively basic model which I can later build upon by adding more parameters to be estimated. I have three .nex files with rRNA, tRNA, and protein-coding gene partitions for 25 species imported into BEAUti, and a relatively simple Birth-Death model wherein

• Clock model (strict) and substitution models (HKY) are unlinked
• Trees are linked across partitions
• Clock rates are to be estimated
  

Unfortunately, I get the rather strange error of treeLikelihoods being NaN. I saw here some information about resolving this type of error, but I have not specified any MRCA priors, or included any time-dependent information (other than the clock rates, which at init values of 0.01 are adequate for the timescales I am interested in (millions of years).

Any suggestions on resolving this type of error?

[Pascale Lubbe]

Well, as it turns out, the problem was that BEUAti in Windows is sometimes buggy, and for whatever reason, the Tree model priors weren't appearing in the Priors box, meaning they were never written into the .xml file. Closing and re-opening BEAUti and creating a new .xml from fresh resolved the issue.