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)
The following error occurs when BEAST is running
Suggestions?
I uploaded my XML - just remove the .png