Log combiner v.2.6.3 trees option

[Maria Eleonora Rossi]

Hi all,

I am trying to use Logcombiner on my server using command line, through BEAST2 installed using Conda, so I am running everything on a conda environment. I looked at the manual but apparently, there is no way to specify the type of file (.trees in this case). 

This is my command: logcombiner -trees ALL_COI_Porifera_withfossils_Aug1.trees ALL_COI_Porifera_withfossils_Aug2.trees ALL_COI_Porifera_withfossils_Aug3.trees -b 20 -resample 10000 -o ALL_COI_Porifera_withfossils_combined.trees

How do I solve this? is logcombiner now only restricted to log files? 

Thank you for your help!

Eleonora

[Remco Bouckaert]

Hi Eleonora,

LogCombiner automatically recognises whether a log file is a trace log or a tree log, so there is no need to specify this separately. You can just use ‘-log’ instead of ‘-trees’ to combined the logs, like so:

logcombiner -log ALL_COI_Porifera_withfossils_Aug1.trees ALL_COI_Porifera_withfossils_Aug2.trees ALL_COI_Porifera_withfossils_Aug3.trees -b 20 -resample 10000 -o ALL_COI_Porifera_withfossils_combined.trees

Cheers,

Remco

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[Emma Wang]

Hi All,

Really need someone's help with logcombinner.

My situation is:

I ran the same xml file on BEAST for twice. Each run, the chain of length is the same, as 200,000,000; every log 20,000. After Beast finished, I got two log files. I tried to combined them into one log file using the command "logcombiner -burnin 20000000 IFV_skygrid_relaxed_run1.log IFV_skygrid_relaxed_run2.log IFV_skygrid_relaxed_combined.log"; I was supposed to see the chain of length in the combined.log was 360,000,000 after burnin 10%. But why I checked the combined.log on Tracer, the chain of length was shown as 360,040,000. I was really confused about that. Could someone help me with this! Really do appreaciate!!!

Thanks!

Emma