TreeAnnotator and MrBayes output

[Hayley Orlowski]

Hello all,

I have been conducting undated total-evidence analyses in MrBayes. MrBayes uses consensus methods (majority-rule by default) to generate a summary tree; I am interested in exploring alternative methods of calculating a summary tree, especially HIPSTR and maximum credibility. 

However, I am having issues with analysing my trees in TreeAnnotator. Sometimes TreeAnnotator will simply stop and close without writing a file; sometimes it will create a file, but not write anything to it (i.e., the file will be blank). In both cases the GUI closes automatically.

 I have successfully analysed my .tre file with target tree type set to Maximum Clade Credibility and no burn-in. The output is normal, albeit with some negative branch lengths; the GUI window shows that the process has been finished and the file written. I tried setting burnin (as states) to 1, and the process completed as normal. However, more realistic values cause the process to fail. Trees are read in, and then the window abruptly closes, with no output file even created.

With no burn-in and target tree set to HIPSTR, the process proceeds to "Annotating target tree", before abruptly closing. In this case an output file is created, but is completely blank (0kb). If a burn-in is specified, the process abruptly terminates as in MCC with no file created.

In all cases I have been using mean heights for node heights.

I am using TreeAnnotator v10.5.0 and MrBayes v3.2.7a.

I have been under the impression that MrBayes output trees can be analysed in TreeAnnotator. Is there an incompatibility between the two that I am not aware of? Can anyone suggest a fix or additional troubleshooting?

Sincerely,

Hayley