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CompEvol / beast2

Bayesian Evolutionary Analysis by Sampling Trees
www.beast2.org
GNU Lesser General Public License v2.1
237 stars 83 forks source link

error in parsing xml with no prior manual editing #1145

Open ptitle opened 6 months ago

ptitle commented 6 months ago

Hi,

I'm posting this issue here, as the documentation on troubleshooting initialization issues requested it, as this may be a bug.

I set up my xml file with BEAUTI, but when I try to run the analysis with BEAST (v2.7.6), I get an xml parsing error. If I then try to open that xml file again with BEAUTI, I get the same xml parsing error and cannot open it anymore.

I haven't touched the xml file otherwise - no manual editing.

I've attached the beast log, and you can download the xml file here.

Any suggestions on how to edit the xml file to get the analysis to run?

Thanks! -Pascal

multiclock.log

ptitle commented 6 months ago

Apologies but I realize that I've overwritten the dropbox file that I linked to here. If one of the developers is interested in exploring this further and would like an xml file that replicates this problem, please let me know.

rbouckaert commented 6 months ago

@ptitle I had a quick look earlier when the file was still available, but could not figure out what happened. Something messy with taxon sets happened, but I could not see an obvious quick way to fix things. If you could make the file available again I can have another look.