BEAUTi adding 1s to taxon IDs (again)

[plubbe]

Hey team-

I've followed the previous threads (#478) on BEAUti adding 1s to taxon IDs, and seen the solution to change the .xml file as so:

replace taxon id="668666_Onth_long_" spec="Taxon”/ with taxon idref="668666_Onth_long_"/

This solution does work, but it is a massive pain, especially when ever-so-slightly changing BEAUti parameters to do multiple runs (for testing clocks, sampling from priors, etc), to change the .xml file every time. I'm still trying to debug priors for calibration nodes, and I can't imagine the only way to get around this problem is by manually editing the 25 taxon IDs every single time I generate a new .xml in BEAUti.

I am running BEAUti/BEASt 2.6.3 at time of writing. Was this bug ever addressed?

[fcsalgado]

same problem here

[rbouckaert]

Unfortunately, I cannot reproduce the problem, so am not quite sure how to fix this. Do you have a reliable way to reproduce the issue?

[plubbe]

Hi @rbouckaert -

Thanks for responding. I haven't tried reliably reproducing the issue, but I for my part it was happening due to the taxon names being too long. I ended up getting around this by just changing the names of all my taxa before importing them into BEAUTi; after I simplified them (down to, say, 10 chars. or so), the issue stopped happening.

[rbouckaert]

Thanks for the hint @plubbe -- perhaps it is possible that truncating taxon name removed some non ascii characters (like brackets, spaces or quotes) that confused taxon name parsing. Were there any such characters in the taxon names?

Another issue is that taxon names of the species cannot be the same as any of one of the gene taxa (issue #135), and BEAUti adds a 1 to the name to make it unique. Could this have been resolved by truncating taxa names?