Help with low values for prior and posterior

[Bruno Alves Sousa Coelho]

Hello all

I'm running several (6 in total) analyses of UCE sequences for 130 taxa, each with 50.000.000 generations, they havent finished yet, most are in the 15mi mark. But looking at the logs with tracer I noticed that most of the parameters reached very high ESS (>1000) very quickly, with the exception of Prior, posterior and the ORCucldMean and ORCSigma, which are still very low (<10). What could be the cause for that?  They barely (if at all) increased from the 5mi mark to 15mi.

We're using a fixed topology through the FixedTree template, the GTR model and normal distribution with multiple fossil calibrators. We also used the Birth-Death model instead of the fixed tree model as it was recommended to us, could that be the problem?

I'm very new to Beast and divergence time calibrations in general. But our objective is to use the ultrametric tree produced in GM analisys (like phylo.integration). Would the low prior and posterior invalidate the tree for this purpose? 

Any help would be much appreciated.

Cheers, Bruno.

[Bruno Alves Sousa Coelho]

Just adding pictures of the log files in tracer

[Artem B]

Hi Bruno,

The traces of ucldMean and sigma should be checked in the first place. It would be good to provide the screenshots.

Best,
Artem

среда, 30 апреля 2025 г. в 02:50:21 UTC+8, Bruno Alves Sousa Coelho: