I am running my dataset via Mr Bayes on XSEDE on CIPRES. Have ran a non-clock analysis, was fine. Then ran a clock analysis (fossilised bd model) with further constraints on key clades (I have morphological data, so I did this to reflect academic consensus reached with molecular data). Then I attempted to calibrate the divergence of said key clades using the estimated divergence dates from a molecular study.
However, I got the error code "Calibrated trees require compatible clockrates but they are incompatible for run 1, chain 1."
I have tried re-running the non-clock analysis with the clade constraints to obtain a better informed clockrate mean (the result of this was very similar to the first clockrate mean I used). Following this I got the same error at the end of my output file:
Division 1 has 116 unique site patterns Initializing conditional likelihoods Using standard non-SSE likelihood calculator for division 1 (single-precision) ERROR: Calibrated trees require compatible clockrates but they are incompatible for run 1, chain 1. Error in command "Mcmc" There was an error on at least one processor The error occurred when reading char. 5-5 on line 124 in the file 'infile.nex'
Returning execution to command line ...
Error in command "Execute"
MrBayes > Deleting previously defined characters Deleting previously defined taxa Quitting program
I have no idea what is wrong. All was working fine before I gave divergence dates for the key clades.
(P.S Please don't rule out that I may have done something very obviously wrong, I am very new to phylogenetics in general and sometimes miss the obvious).
