Starting tree generation has failed: null

[A Brito]

Hi,

I'm facing a Beauti issue for which I couldn't find a solution in this forum yet.

I'm trying to generate an XML for BEASTv1.10.4 on Mac (please see the Beauti raw text, and failed XML attached below). I'm setting a run with 87 taxa, 1 partition, "Tip date sampling", UCLN clock model, and MLE by PS/SS. When I try to "Generate BEAST file...", I've been getting the error message below (see screenshot attached below).

I have already re-installed the latest version of Beast/Beauti, but the issue persists. Attached below I also sent a Java error related to this issue:

objc[5153]: Class FIFinderSyncExtensionHost is implemented in both /System/Library/PrivateFrameworks/FinderKit.framework/Versions/A/FinderKit (0x7fff99c5a3c8) and /System/Library/PrivateFrameworks/FileProvider.framework/OverrideBundles/FinderSyncCollaborationFileProviderOverride.bundle/Contents/MacOS/FinderSyncCollaborationFileProviderOverride (0x19e296f50). One of the two will be used. Which one is undefined.

(...)

dr.app.beauti.generator.Generator$GeneratorException: Starting tree generation has failed:

Does anyone know a solution for this issue?

Best,

Anderson Brito

[A Brito]

Hi,

I found out what was causing this issue: it has something to do with the functionality used to "Import Taxon Set.

If you want to specify a taxa set for tip date sampling, one can import the taxa with uncertain dates using "Import Taxon Set" (importing a text file with the tip names). It seems Beauti has not been able to recognize the imported information (see first image attached below).

If one removes a taxon from the right side panel, and puts it back, the number of selected taxa gets updated, but still, Beauti is not able to export the XML properly (see second image).

The solution so far has been to select and add the taxa set manually, instead of importing their tip names from an external file.

Best,

Anderson

[Martin Paliocha]

Hey Anderson,

thank you so much for your answer, I experienced the same issue but I finally got it to work!

Best,

Martin

[A Brito]

You're welcome! This forum is really useful.

I came across the same issue again today. I forgot how to solve that, and 'googled' the error message in this forum... boom!

I've just answered my own question. Yep, embarrassing and rewarding at the same time.

Best,

[Lucía Graña]

Have the same problem but making the partition manually is not an option, did anyone find another solution for this?

[Lambodhar Damodaran]

Hey everyone,

I had the same issue, I ended up just putting in a single dummy taxon set manually in BEAUTI and then opening my XML file in a text editor and duplicating the fields relating to it.editing the sets as needed for my specific taxon sets. After doing that I was able to run my xml without issue. Hopefully this can help someone with the same issue, BEAUTI has yet to be fixed to deal with this issue.

[Miguel Mendez Sandin]

Hey,

Same issue here. And importing/adding taxa manually is of a quite time-consuming task (~10,000 taxa and ~50 sets...)