Questions about combining log files and trees files on Logcombiner

[Emma Wang]

Dear All,

Really need someone could help me with the logcombiner. I was stuck on this point for several days and really did not know how I should do. 

My situation is:

I ran the same xml files on BEAST for twice. The chain of length is 200,000,000; every log 20,000. In order to get the better ESS values, I need to combine these two runs. So I tried to use logcombiner command to combine two log.files generated from BEAST step. The code I use is below. The question is - I was supposed to get the combined file with 360,000,000 chain of length after burnin 10%, right? But after running the below command, I checked the combined file in Tracer, it showed that the chain of length was 360,040,000. I was quite confused how we got this extra 40000? Could someone help me to understand this logic here? 

$ logcombiner -burnin 20000000 IFV_skygrid_relaxed_run1.log IFV_skygrid_relaxed_run2.log IFV_skygrid_relaxed_combined.log

Another question is about how to combine the trees.file from these two runs using logcombiner? Could I use the same command as the above to combine trees.file? But how do we specify the burnin for trees. files? Really do appreaciate if someone could help me with this!

[Mark Miller]

Hi Emma,

I can't find a user with your email account.

Can you please send me the username on your account, or else the file _jobinfo.txt from your job run?

Mark