Issues with Treeannotator 2.7.7

[lilychughes]

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?

[rbouckaert]

When using the lowMem option a value of true or false is expected in BEAST v2.7. If you try

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

it should work.

By the way, it is recommended to install the CCD package and use the CCD0 topology option. From the command line, use:

treeannotator -topology CCD0 -burnin 20 -lowMem true input.trees out.tre

or if you are lazy, any command line option can be abbreviated to the first letters (as long as they are unique), for example like so:

treeannotator -t CCD0 -b 20 -l true input.trees out.tre

which is not much longer than you were used to. Hope this helps, Remco