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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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v1.10.4 Error parsing '<treeDataLikelihood>' element with id, 'default.treeLikelihood': #1176

Closed xinaoma closed 5 months ago

xinaoma commented 5 months ago

The following error occurs when BEAST is running

 BEAST v1.10.4 Prerelease #bc6cbd9, 2002-2018
       Bayesian Evolutionary Analysis Sampling Trees
                 Designed and developed by
   Alexei J. Drummond, Andrew Rambaut and Marc A. Suchard

               Department of Computer Science
                   University of Auckland
                  alexei@cs.auckland.ac.nz

             Institute of Evolutionary Biology
                  University of Edinburgh
                     a.rambaut@ed.ac.uk

              David Geffen School of Medicine
           University of California, Los Angeles
                     msuchard@ucla.edu

                Downloads, Help & Resources:
                    http://beast.community

Source code distributed under the GNU Lesser General Public License:
            http://github.com/beast-dev/beast-mcmc

                     BEAST developers:
    Alex Alekseyenko, Guy Baele, Trevor Bedford, Filip Bielejec, Erik Bloomquist, Matthew Hall,
    Joseph Heled, Sebastian Hoehna, Denise Kuehnert, Philippe Lemey, Wai Lok Sibon Li,
    Gerton Lunter, Sidney Markowitz, Vladimir Minin, Michael Defoin Platel,
            Oliver Pybus, Chieh-Hsi Wu, Walter Xie

                         Thanks to:
        Roald Forsberg, Beth Shapiro and Korbinian Strimmer

Using BEAGLE library v4.0.0 (PRE-RELEASE) for accelerated, parallel likelihood evaluation
2009-, BEAGLE Working Group - https://beagle-dev.github.io/
Citation: Ayres et al (2019) Systematic Biology 68: 1052-1061 | doi:10.1093/sysbio/syz020

Random number seed: 1713776027614

Loading additional development parsers from development_parsers.properties, which is additional set of parsers only available for development version ...
Parsing XML file: PSV-didian.xml
  File encoding: GBK
Looking for plugins in C:\Users\18493\Desktop\plugins

Read alignment: alignment
  Sequences = 143
      Sites = 8522
   Datatype = nucleotide
Site patterns 'patterns' created from positions 1-8522 of alignment 'alignment'
  unique pattern count = 3452
Read attribute patterns, 'locations.pattern' for attribute, locations

Creating the tree model, 'treeModel'
  taxon count = 147
  tree height = 2057.255888732665
Bayesian skyline plot: 10 stepwise control points
Exponential markov model on parameter skyline.popSize (jeffreys=true, reverse=false)

Using discretized relaxed clock model.
  over sampling = 1
  parametric model = logNormalDistributionModel
   rate categories = 1

Using strict molecular clock model.

Creating state frequencies model 'frequencies': Initial frequencies = {0.25, 0.25, 0.25, 0.25}

Creating site rate model: 
  4 category discrete gamma with initial shape = 0.5

BEAST has terminated with an error. Please select QUIT from the menu.
Apr 22, 2024 4:53:54 PM dr.app.beast.BeastMain <init>
SEVERE: Parsing error - poorly formed BEAST file, PSV-didian.xml:
Error parsing '<treeDataLikelihood>' element with id, 'default.treeLikelihood':
TreeModel contains more taxa than the partition pattern list.

Error thrown at: dr.evomodelxml.treedatalikelihood.TreeDataLikelihoodParser.createTreeDataLikelihood(Unknown Source)

PSV xml Suggestions?

I uploaded my XML - just remove the .png