Dear all,
I need to combine .t files from a MrBayes analysis. Using mcmcp, sumt, and sump commands is not an option, since due to CIPRES analytical limitations I need to combine files from 2 different analyses.
I tried to import each .t files from the two independent analyses in LogCombiner (total: 4 .t files) but I had error message:
Exception: / by zero
Finished - Quit program to exit.
java.lang.ArithmeticException: / by zero
at beast.app.tools.LogCombiner.readTreeLogFile(Unknown Source)
at beast.app.tools.LogCombiner.combineLogs(Unknown Source)
at beast.app.tools.LogCombiner.main(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at beast.app.beastapp.BeastLauncher.run(Unknown Source)
at beast.app.tools.LogCombinerLauncher.main(Unknown Source)
Also, it fails to load all the 4 files. Does anyone has an idea how to fix this error? Is there any alternative to LogCombiner?
Thanks in advance
Filippo
Hi Filippo,
Check this out:
https://groups.google.com/g/beast-users/c/Mft03TQ_l7c
They explain a little about your issue.
Israel
Hey,
you can try to do it in R. This should work:
library(ape)
read.nexus(file="~/file.name1.trees") -> run1 #first run
read.nexus(file="~/file.name2.trees") -> run2 #second run
c(run1[10:100], run2[10:100]) -> cmb #adjust numbers to set your burn-in
write.nexus(cmb, file = "~/cmb.trees") #write file
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