Problem of calibrate dating in BEAST

[orochi1...@gmail.com]

Dear BEAST developers, I am currently using BEAST to do Calibrate dating by some known node age, here r the error message that pop up from BEAST window. Can any one help to sort out the problem, I am stuck here in this stage. Thanks so much!

Below r the error message:

                        BEAST v2.4.8, 2002-2017

             Bayesian Evolutionary Analysis Sampling Trees

                       Designed and developed by

 Remco Bouckaert, Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard

                                    

                     Department of Computer Science

                         University of Auckland

                        re...@cs.auckland.ac.nz

                        ale...@cs.auckland.ac.nz

                                    

                   Institute of Evolutionary Biology

                        University of Edinburgh

                           a.ra...@ed.ac.uk

                                    

                    David Geffen School of Medicine

                 University of California, Los Angeles

                           msuc...@ucla.edu

                                    

                      Downloads, Help & Resources:

                           http://beast2.org/

                                    

  Source code distributed under the GNU Lesser General Public License:

                   http://github.com/CompEvol/beast2

                                    

                           BEAST developers:

   Alex Alekseyenko, Trevor Bedford, Erik Bloomquist, 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

Random number seed: 1518730167676

Alignment(ND4 final 2018new_with outgroup)

  256 taxa

  786 sites

  309 patterns

  UCRelaxedClockModel: using 510 rate categories to approximate rate distribution across branches.

TreeLikelihood(treeLikelihood.ND4 final 2018new_with outgroup0) uses BeerLikelihoodCore4

  Alignment(ND4 final 2018new_with outgroup): [taxa, patterns, sites] = [256, 309, 786]

Alignment(ALIGNMENT 12S_2018_01_31 final)

  256 taxa

  407 sites

  114 patterns

  UCRelaxedClockModel: using 510 rate categories to approximate rate distribution across branches.

TreeLikelihood(treeLikelihood.ALIGNMENT 12S_2018_01_31 final0) uses BeerLikelihoodCore4

  Alignment(ALIGNMENT 12S_2018_01_31 final): [taxa, patterns, sites] = [256, 114, 407]

Error 110 parsing the xml input file

validate and intialize error: Cannot use originate of root. You can set useOriginate to false to fix this

Error detected about here:

  <beast>

      <run id='mcmc' spec='MCMC'>

          <distribution id='posterior' spec='util.CompoundDistribution'>

              <distribution id='fossilCalibrations' spec='util.CompoundDistribution'>

                  <distribution id='root.fossilprior' spec='beast.math.distributions.FossilPrior'>

Failed to load BEAGLE library: no hmsbeagle-jni in java.library.path

Failed to load BEAGLE library: no hmsbeagle-jni in java.library.path

java.lang.IllegalArgumentException: Cannot use originate of root. You can set useOriginate to false to fix this

at beast.math.distributions.MRCAPrior.initAndValidate(Unknown Source)

at beast.math.distributions.FossilPrior.initAndValidate(Unknown Source)

at beast.util.XMLParser.initBEASTObjects(Unknown Source)

at beast.util.XMLParser.parse(Unknown Source)

at beast.util.XMLParser.parseFile(Unknown Source)

at beast.app.BeastMCMC.parseArgs(Unknown Source)

at beast.app.beastapp.BeastMain.main(Unknown Source)

at beast.app.beastapp.BeastLauncher.main(Unknown Source)

[Remco Bouckaert]

The FossilPrior makes only sense as a distribution on the originate of a clade. Since the root has no originate, it does not make sense to use it as a calibration for the root. You could replace it with an MRCAPrior on the root if you still want to use that calibration.

Cheers, Remco

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<D2_namecode.xml>

[orochi1...@gmail.com]

Many thx

在 2018年2月19日星期一 UTC+2上午4:22:56，Remco Bouckaert写道：