Can't Link Site model Beast 2.4.2/2.4.3

[Jason Strickland]

Hello Beast Community,

I have been using the Beast 2.3.2 package for the last year but switched to 2.4.3 for my current analyses. I am trying to link site models and, for whatever reason, Beauti is not allowing me in either 2.4.2 or 2.4.3. I tried simply linking the two genes by highlighting both and clicking the link site model button as well as changing them using the drop down. I can do it fine in 2.3.2 both ways but will not work in 2.4. I created a file with limited taxa and only two genes (attached) as a test and I can't get that one to do it either. Please let me know if I am making a silly mistake or if it is something else.

Cheers,

Jason Strickland

Ph.D. Candidate - Parkinson Lab

University of Central Florida

[Remco Bouckaert]

Hi Jason,

With the nexus file you posted, I had no problem linking the site models in 2.4.3, so perhaps there is something in your setup that blocks linking. What packages do you have installed? Can you try the following: start BEAUti, import the nexus file, try to link the site models and then click Help/Messages. A dialog pops up showing potential problems.

Cheers,

Remco

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<SiteModelLinkTest.nex>

[Jason Strickland]

Hi Remco,

Thank you for the quick response. I did what you asked and have attached the full file from messages. I have pasted below the relevant portion that shows up once I try to link the site models. I checked my packages and some were not updated so I updated them and tried again.  The same error came up. I have all packages installed currently. I am using Beast for Windows. 

PARTITIONS:

[[0, 1], [0, 1], [0, 1]]

WARNING: multiple beastObjects match, but hasPartitions=none

updateModel: 1 5 0 0

0 ND4 ND4 ND4 ND4

1 NT3 ND4 NT3 NT3

Cannot link site model: substitution models are incompatible

updateModel: 1 5 0 0

0 ND4 ND4 ND4 ND4

1 NT3 NT3 NT3 NT3

updateModel: 1 5 0 0

0 ND4 ND4 ND4 ND4

1 NT3 ND4 NT3 NT3

Let me know if that is helpful or if you need additional information. 

Thanks,

Jason

[Remco Bouckaert]

Hi Jason,

Thanks for the information — that is very useful. The test file you sent had nucleotides in them, while the log shows that the LG substitution model was selected, which is an amino acid model. Are you using the Standard template? Can you change the substitution model for each of the partitions to a nucleotide substitution model (in the site model panel) and link after that?

Cheers,

Remco

<SiteModelLinkMessages.txt>

[Jason Strickland]

Hi Remco,

Yes, I am using the standard template. When I import the alignment, the data type comes up as nucleotide (1st attachment). When I go to the Site Model tab, the models I can select are the nucleotide models not the amino acid models (second attachment). Then, once I put the model the same for both loci, I am able to link them. I played around with it and once I make them the same one time, I can link/unlink and change the model however I want and it responds as expected. Thank you very much for your help trouble shooting. 

Cheers,

Jason

[Remco Bouckaert]

Hi Jason,

Thanks for confirming this workaround solves the problem — BEAUti should pick a nucleotide substitution model by default so I will investigate further to see why this does not happen.

Cheers,

Remco

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