Question: MrBayes chains converged, how to stop early?
0
gravatar for Adrian Pelin
4.0 years ago by
Adrian Pelin2.3k
Canada
Adrian Pelin2.3k wrote:

Hello,

My run is programmed for 5000000 MCMC steps, but it looks like it's converging early

Average standard deviation of split frequencies: 0.008884

      1726000 -- [-112794.860] [...15 remote chains...] -- 32:50:30
      1727000 -- [-112792.714] [...15 remote chains...] -- 32:50:20
      1728000 -- (-112794.589) [...15 remote chains...] -- 32:50:08
      1729000 -- [-112808.611] [...15 remote chains...] -- 32:49:56

Any way to stop this early? Or is it best to let it converge more?

Adrian

 

bayesian mrbayes phylogeny • 3.1k views
ADD COMMENTlink modified 4.0 years ago by qiyunzhu130 • written 4.0 years ago by Adrian Pelin2.3k
1
gravatar for qiyunzhu
4.0 years ago by
qiyunzhu130
United States
qiyunzhu130 wrote:

Ctrl + C will do the job.

Then you need to manually add footers to the output files, *.t and *.p, to make them intact.

Then you can go back to MrBayes and do sump.

ADD COMMENTlink written 4.0 years ago by qiyunzhu130

seems like just adding end; at end of *.t files worked. Thanks! I wish there was an easier way to do this.

ADD REPLYlink written 4.0 years ago by Adrian Pelin2.3k
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