java.lang.RuntimeException: Cannot find taxon 1-78 in data

[Yanina Briñoccoli]

Hi everyone,

I'm trying to run BEAST for the first time but I couldn't solve this error:

java.lang.RuntimeException: Cannot find taxon 1-78 in data
at beast.base.evolution.tree.MRCAPrior.initialise(Unknown Source)
at beast.base.evolution.tree.MRCAPrior.calculateLogP(Unknown Source)
at beast.base.inference.CompoundDistribution.calculateLogP(Unknown Source)
at beast.base.inference.CompoundDistribution.calculateLogP(Unknown Source)
at beast.base.inference.State.robustlyCalcPosterior(Unknown Source)
at beast.base.inference.MCMC.run(Unknown Source)
at beastfx.app.beast.BeastMCMC.run(Unknown Source)
at beastfx.app.beast.Controller$2.run(Unknown Source)

Could someone help me? I attached the xml: https://drive.google.com/file/d/14LwCUaRMWtSmw68m7Ke5DLDyrWHzZy1D/view?usp=drive_link

Thanks,

Yanina

[Gaspary Eugene]

Hi,

can you check if the correct  sequence name "1-78"  in your fasta/nexus may contain  special characters? scan quickly for this taxon name and rectify in Aliview?

Gaspary

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[Gaspary Eugene]

Looks like your sequence data contains a taxon name 

<distribution id="Pop_1.prior" spec="beast.base.evolution.tree.MRCAPrior" monophyletic="true" tree="@Tree.nex-jun24">

                                    
                    <taxonset id="Pop_1" spec="TaxonSet">
                                            
                        <taxon id="1-78" spec="Taxon"/>

From your XML file,  it seems the taxon name is "Pop_1" but your alignment sequence contains "1-78" that do not match ......

Open the sequence data and correct the name choose "Pop_1" or "1-78" and recreate the xml file again and when you re-run make sure you modify the name of the xml or if you run on terminal you can include -overwrite options to continue the previous run and overwrite the existing log and tree files

Gaspary  

On Wed, Jun 19, 2024 at 10:23 PM Yanina Briñoccoli <ybrin...@gmail.com> wrote:

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[Yanina Briñoccoli]

Thank you very much!
The mistake was that there is no sequence "1-78" as such, but that the alignment contained 78 individuals, in two populations "b" and "m".

In case it helps anyone else, the correction was:

<distribution id="Pop_1.prior" spec="beast.base.evolution.tree.MRCAPrior" monophyletic="true" tree="@Tree.nex-jun24">

  <taxonset id="Pop_1" spec="TaxonSet">

      <taxon idref="m"/>

      <taxon idref="b"/>