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Issues with Treeannotator 2.7.7

Open lilychughes opened this issue 8 months ago • 1 comments

Hi,

Longtime BEAST2 user here! I just updated to the latest version of everything, and I am suddenly having issues with Treeannotator (command line) that I have never had before. First, when I look at the documentation, I see this at the top:

Usage: beastfx.app.treeannotator.TreeAnnotator
Not documented!!!

I have typically run treeannotator in the past something like this, where out.tre is the output file:

treeannotator -burnin 20 -lowMem input.trees out.tre

But now I am getting an error that suggests treeannotator is looking for out.tre as an input file:

Error Parsing Input Tree: out.tre (No such file or directory)

There seems to be no way to specify an output file anymore? It only writes to stdout?

lilychughes avatar Feb 04 '25 21:02 lilychughes