MrBayes chains converged, how to stop early?

Question

[Adrian Pelin]

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

Answer 1

[qiyunzhu]

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.

[Adrian Pelin]

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

[dongzhang0725]

You can try PhyloSuite, see step 8 in the example: http://phylosuite.jushengwu.com/dongzhang0725.github.io/documentation/#5-12-1-Brief-example