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beast-dev / beast-mcmc

Bayesian Evolutionary Analysis Sampling Trees
http://beast.community
GNU Lesser General Public License v2.1
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Tree prior generation has failed: Index 5 out of bounds for length 5 #1113

Closed niconm89 closed 3 years ago

niconm89 commented 3 years ago

Hi, I'm trying to generate a matrix file using beauti but I got an error in the final step.

Here are the steps I'm following.

1) I have 51 partitions (12 taxa), I have only selected unlink site models, link clock model and link trees.

2) I selected a specific site model for each partition

3) I selected an uncorrelated relaxed clock with a lognormal distribution

4) I selected 'Speciation: Birth-Death Process' as Tree prior

5) I define a molecular clock in the Priors section

Finally, when I click on generate BEAST file, I got the error "The BEAST XML is incomplete because: Tree prior generation has failed: Index 5 out of bounds for length 5"

I tried to fix it by deleting some partitions and choosing other Tree priors but nothing changed.

I appreciate any help you can give me.

Nicolás

GuyBaele commented 3 years ago

This should have been fixed in the meantime in commit: https://github.com/beast-dev/beast-mcmc/commit/d19f2f59ac05311c524f187a9579952feeabfd31

I can send you an updated beast.jar file that has this fix, or you could build one as well.

Best regards, Guy

niconm89 commented 3 years ago

Thank you Guy, I built a beast.jar and now it is working.

LesterJP commented 3 years ago

Hi, Guy I am trying ot generate the XML to perform a phylogeographic analysis using the travel history model, every time I tried to generate the XML using beauti 1.10.5pre_thorney_0.1.1 I got an error in the final step.

He "The BEAST XML is incomplete because Taxon list generation has failed: Index 5 out of bounds for length 5" I appreciate any help you can give me. Lester

v-julia commented 2 years ago

Hi, Guy.

I have the same error. In some of my sequences there is no info on sampling day, so I use parsing calendar dates with variable precision. No partition into codon position, strict clock. I need 'Speciation: Birth-Death Process' tree prior for my analysis, but I also tried the other ones. And every time I am getting "The BEAST xml is incomplete because: Taxon list generation has failed: 5". Am I doing something wrong?

v1.10.5pre_thorney_v0.1.2 Windows 10