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Failed run beast v2.6.3 using test1.xml in STAECY v1.2.5 pacakage

Bioinformatics Asked on May 19, 2021

I am using the package STAECY v1.2.5 in beast v2.6.3. But it failed in testing the test1.xml in STACEY example package. I am attaching the beast running log below.

    BEAST v2.6.3, 2002-2020
             Bayesian Evolutionary Analysis Sampling Trees
                       Designed and developed by
 Remco Bouckaert, Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard
                                    
                   Centre for Computational Evolution
                         University of Auckland
                       [email protected]
                        [email protected]
                                    
                   Institute of Evolutionary Biology
                        University of Edinburgh
                           [email protected]
                                    
                    David Geffen School of Medicine
                 University of California, Los Angeles
                           [email protected]
                                    
                      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, Tim Vaughan, Chieh-Hsi Wu, Walter Xie
                                    
                               Thanks to:
          Roald Forsberg, Beth Shapiro and Korbinian Strimmer

Random number seed: 1614835287667

a01_A: 500 4
a02_A: 500 4
a03_A: 500 4
a04_A: 500 4
a05_A: 500 4
b01_A: 500 4
b02_A: 500 4
b03_A: 500 4
b04_A: 500 4
b05_A: 500 4
c01_A: 500 4
c02_A: 500 4
c03_A: 500 4
c04_A: 500 4
c05_A: 500 4
Alignment(U2SQg5t10r1-4)
  15 taxa
  500 sites
  13 patterns

a01_A: 500 4
a02_A: 500 4
a03_A: 500 4
a04_A: 500 4
a05_A: 500 4
b01_A: 500 4
b02_A: 500 4
b03_A: 500 4
b04_A: 500 4
b05_A: 500 4
c01_A: 500 4
c02_A: 500 4
c03_A: 500 4
c04_A: 500 4
c05_A: 500 4
Alignment(U2SQg5t10r1-5)
  15 taxa
  500 sites
  11 patterns

a01_A: 500 4
a02_A: 500 4
a03_A: 500 4
a04_A: 500 4
a05_A: 500 4
b01_A: 500 4
b02_A: 500 4
b03_A: 500 4
b04_A: 500 4
b05_A: 500 4
c01_A: 500 4
c02_A: 500 4
c03_A: 500 4
c04_A: 500 4
c05_A: 500 4
Alignment(U2SQg5t10r1-2)
  15 taxa
  500 sites
  15 patterns

a01_A: 500 4
a02_A: 500 4
a03_A: 500 4
a04_A: 500 4
a05_A: 500 4
b01_A: 500 4
b02_A: 500 4
b03_A: 500 4
b04_A: 500 4
b05_A: 500 4
c01_A: 500 4
c02_A: 500 4
c03_A: 500 4
c04_A: 500 4
c05_A: 500 4
Alignment(U2SQg5t10r1-3)
  15 taxa
  500 sites
  17 patterns

a01_A: 500 4
a02_A: 500 4
a03_A: 500 4
a04_A: 500 4
a05_A: 500 4
b01_A: 500 4
b02_A: 500 4
b03_A: 500 4
b04_A: 500 4
b05_A: 500 4
c01_A: 500 4
c02_A: 500 4
c03_A: 500 4
c04_A: 500 4
c05_A: 500 4
Alignment(U2SQg5t10r1-1)
  15 taxa
  500 sites
  12 patterns

Failed to load BEAGLE library: no hmsbeagle64 in java.library.path: C:Program FilesJavajdk-15bin;C:WINDOWSSunJavabin;C:WINDOWSsystem32;C:WINDOWS;C:Perl64bin;C:UserschenyAppDataRoamingActiveStatebin;C:Rtoolsbin;C:Program Files (x86)Common FilesOracleJavajavapath;C:Program FilesCommon FilesOracleJavajavapath;C:WINDOWSsystem32;C:WINDOWS;C:WINDOWSSystem32Wbem;C:WINDOWSSystem32WindowsPowerShellv1.0;C:WINDOWSSystem32OpenSSH;C:Program FilesPuTTY;C:Program FilesMEGA-X;C:Program FilesPandoc;C:CTEXUserDatamiktexbin;C:CTEXMiKTeXmiktexbin;C:CTEXCTeXctexbin;C:CTEXCTeXcctbin;C:CTEXCTeXtybin;C:CTEXGhostscriptgs9.05bin;C:CTEXGSviewgsview;C:CTEXWinEdt;C:Program Filesmingw-w64x86_64-8.1.0-posix-seh-rt_v6-rev0mingw64bin;C:ProgramDatachocolateybin;C:UserschenyAppDataRoamingPythonPython38Scripts;C:Program FilesGitcmd;C:Program FilesRR-3.6.3bin;G:appsPTPbin;C:UserschenyBEAST2.6;C:UserschenyAppDataLocalProgramsPythoTreeLikelihood(treeLikelihood.U2SQg5t10r1-1) uses BeerLikelihoodCore4
  Alignment(U2SQg5t10r1-1): [taxa, patterns, sites] = [15, 12, 500]
nPython38Scripts;C:UserschenyAppDataLocalProgramsPythonPython38;C:UserschenyAppDataLocalGitHubDesktopbin;C:UserschenyAppDataLocalProgramsMicrosoft VS Codebin;C:UserschenyAppDataRoamingTinyTeXbinwin32;G:appsBMGE-1.12;C:Program FilesJavajdk-15bin;.
Failed to load BEAGLE library: no hmsbeagle64 in java.library.path: C:Program FilesJavajdk-15bin;C:WINDOWSSunJavabin;C:WINDOWSsystem32;C:WINDOWS;C:Perl64bin;C:UserschenyAppDataRoamingActiveStatebin;C:Rtoolsbin;C:Program Files (x86)Common FilesOracleJavajavapath;C:Program FilesCommon FilesOracleJavajavapath;C:WINDOWSsystem32;C:WINDOWS;C:WINDOWSSystem32Wbem;C:WINDOWSSystem32WindowsPowerShellv1.0;C:WINDOWSSystem32OpenSSH;C:Program FilesPuTTY;C:Program FilesMEGA-X;C:Program FilesPandoc;C:CTEXUserDatamiktexbin;C:CTEXMiKTeXmiktexbin;C:CTEXCTeXctexbin;C:CTEXCTeXcctbin;C:CTEXCTeXtybin;C:CTEXGhostscriptgs9.05bin;C:CTEXGSviewgsview;C:CTEXWinEdt;C:Program FiTreeLikelihood(treeLikelihood.U2SQg5t10r1-2) uses BeerLikelihoodCore4
  Alignment(U2SQg5t10r1-2): [taxa, patterns, sites] = [15, 15, 500]
lesmingw-w64x86_64-8.1.0-posix-seh-rt_v6-rev0mingw64bin;C:ProgramDatachocolateybin;C:UserschenyAppDataRoamingPythonPython38Scripts;C:Program FilesGitcmd;C:Program FilesRR-3.6.3bin;G:appsPTPbin;C:UserschenyBEAST2.6;C:UserschenyAppDataLocalProgramsPythonPython38Scripts;C:UserschenyAppDataLocalProgramsPythonPython38;C:UserschenyAppDataLocalGitHubDesktopbin;C:UserschenyAppDataLocalProgramsMicrosoft VS Codebin;C:UserschenyAppDataRoamingTinyTeXbinwin32;G:appsBMGE-1.12;C:Program FilesJavajdk-15bin;.
Failed to load BEAGLE library: no hmsbeagle64 in java.library.path: C:Program FilesJavajdk-15bin;C:WINDOWSSunJavabin;C:WINDOWSsystem32;C:WINDOWS;C:Perl64bin;C:UserschenyAppDataRoamingActiveStatebin;C:Rtoolsbin;C:Program Files (x86)Common FilesOracleJavajavapath;C:Program FilesCommon FilesOracleJavajavapath;C:WINDOWSsystem32;C:WINDOWS;C:WINDOWSSystem32Wbem;C:WINDOWSSystem32WindowsPowerShellv1.0;C:WINDOWSSystem32OpenSSH;C:Program FilesPuTTY;C:Program FilesMEGA-X;C:Program FilesPandoc;C:CTEXUserDatamiktexbin;C:CTEXMiKTeXmiktexbin;C:CTEXCTeXctexbin;C:CTEXCTeXcctbin;C:CTEXCTeXtybin;C:CTEXGhostscriptgs9.05bin;C:CTEXGSviewgsview;C:CTEXWinEdt;C:Program Filesmingw-w64x86_64-8.1.0-posix-seh-rt_v6-rev0mingw64bin;C:ProgramDatachocolateybin;C:UserschenyAppDataRoamingPythonPython38Scripts;C:Program FilesGitcmd;C:Program FilesRR-3.6.3bin;G:appsPTPbin;C:UserschenyBEAST2.6;C:UserschenyAppDataLocalProgramsPythonPython38Scripts;C:UserschenyAppDataLocalProgramsPythonPython38;C:UserschenyAppDataLocalGitHubDesktopbin;C:UserschenyAppDataLocalProgramsMicrosoft VS Codebin;C:UserschenyAppDataRoamingTinyTeXbinwin32;G:appsBMGE-1.12;C:Program FilesJavajdk-15bin;.
Failed to load BEAGLE library: no hmsbeagle64 in java.library.path: C:Program FilesJavajdk-15bin;C:WINDOWSSunJavabin;C:WINDOWSsystem32;C:WINDOWS;C:Perl64binTreeLikelihood(treeLikelihood.U2SQg5t10r1-3) uses BeerLikelihoodCore4
  Alignment(U2SQg5t10r1-3): [taxa, patterns, sites] = [15, 17, 500]
;C:UserschenyAppDataRoamingActiveStatebin;C:Rtoolsbin;C:Program Files (x86)Common FilesOracleJavajavapath;C:Program FilesCommon FilesOracleJavajavapath;C:WINDOWSsystem32;C:WINDOWS;C:WINDOWSSystem32Wbem;C:WINDOWSSystem32WindowsPowerShellv1.0;C:WINDOWSSystem32OpenSSH;C:Program FilesPuTTY;C:Program FilesMEGA-X;C:Program FilesPandoc;C:CTEXUserDatamiktexbin;C:CTEXMiKTeXmiktexbin;C:CTEXCTeXctexbin;C:CTEXCTeXcctbin;C:CTEXCTeXtybin;C:CTEXGhostscriptgs9.05bin;C:CTEXGSviewgsview;C:CTEXWinEdt;C:Program Filesmingw-w64x86_64-8.1.0-posix-seh-rt_v6-rev0mingw64bin;C:ProgramDatachocolateybin;C:UserschenyAppDataRoamingPythonPython38Scripts;C:Program FilesGitcmd;C:Program FilesRR-3.6.3bin;G:appsPTPbin;C:UserschenyBEAST2.6;C:UserschenyAppDataLocalProgramsPythonPython38Scripts;C:UserschenyAppDataLocalProgramsPythonPython38;C:UserschenyAppDataLocalGitHubDesktopbin;C:UserschenyAppDataLocalProgramsMicrosoft VS Codebin;C:UserschenyAppDataRoamingTinyTeXbinwin32;G:appsBMGE-1.12;C:Program FilesJavajdk-15bin;.
Failed to load BEAGLE library: no hmsbeagle64 in java.library.path: C:Program FilesJavajdk-15bin;C:WINDOWSSunJavabin;C:WINDOWSsystem32;C:WINDOWS;C:Perl64bin;C:UserschenyAppDataRoamingActiveStatebin;C:Rtoolsbin;C:Program Files (x86)Common FilesOracleJavajavapath;C:Program FilesCommon FilesOracleJavajavapath;C:WINDOWSsystem32;C:WINDOWS;C:WINDOWSSystem32Wbem;C:WINDOWSSystem32WindowsPowerShellv1.0;C:WINDOWSSystem32OpenSSH;C:Program FilesPuTTY;C:Program FilesMEGA-X;C:Program FilesPandoc;C:CTEXUserDatamiktexbin;C:CTEXMiKTeXmiktexbin;C:CTEXCTeXctexbin;C:CTEXCTeXcctbin;C:CTEXCTeXtybin;C:CTEXGhostscriptgs9.05bin;C:CTEXGSviewgsview;C:CTEXWinEdt;C:Program Filesmingw-w64x86_64-8.1.0-posix-seh-rt_v6-rev0mingw64bin;C:ProgramDatachocolateybin;C:UserschenyAppDataRoamingPythonPython38Scripts;C:Program FilesGitcmdTreeLikelihood(treeLikelihood.U2SQg5t10r1-4) uses BeerLikelihoodCore4
  Alignment(U2SQg5t10r1-4): [taxa, patterns, sites] = [15, 13, 500]
;C:Program FilesRR-3.6.3bin;G:appsPTPbin;C:UserschenyBEAST2.6;C:UserschenyAppDataLocalProgramsPythonPython38Scripts;C:UserschenyAppDataLocalProgramsPythonPython38;C:UserschenyAppDataLocalGitHubDesktopbin;C:UserschenyAppDataLocalProgramsMicrosoft VS Codebin;C:UserschenyAppDataRoamingTinyTeXbinwin32;G:appsBMGE-1.12;C:Program FilesJavajdk-15bin;.
TreeLikelihood(treeLikelihood.U2SQg5t10r1-5) uses BeerLikelihoodCore4
  Alignment(U2SQg5t10r1-5): [taxa, patterns, sites] = [15, 11, 500]
===============================================================================
Citations for this model:

Bouckaert, Remco, Timothy G. Vaughan, Joëlle Barido-Sottani, Sebastián Duchêne, Mathieu Fourment, 
Alexandra Gavryushkina, Joseph Heled, Graham Jones, Denise Kühnert, Nicola De Maio, Michael Matschiner, 
Fábio K. Mendes, Nicola F. Müller, Huw A. Ogilvie, Louis du Plessis, Alex Popinga, Andrew Rambaut, 
David Rasmussen, Igor Siveroni, Marc A. Suchard, Chieh-Hsi Wu, Dong Xie, Chi Zhang, Tanja Stadler, 
Alexei J. Drummond 
  BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. 
  PLoS computational biology 15, no. 4 (2019): e1006650.

Graham Jones (2016). Algorithmic improvements to species delimitation and phylogeny estimation under the multispecies coalescent.
Journal of Mathematical Biology. DOI 10.1007/s00285-016-1034-0
http://link.springer.com/article/10.1007/s00285-016-1034-0 

Jones GR, Aydin Z, and Oxelman B (2015). DISSECT: an assignment-free Bayesian discovery method for species delimitation under the multispecies coalescent.
Bioinformatics 31 (7) 991-998. DOI 10.1101/003178
http://bioinformatics.oxfordjournals.org/content/31/7/991.

===============================================================================
Start likelihood: -Infinity after 10 initialisation attempts
P(posterior) = -Infinity (was -Infinity)
    P(smcCoalescent) = -Infinity (was -Infinity)
    P(prior) = NaN (was NaN)  **
        P(BirthDeathCollapseModel.t:Species) = NaN (was NaN)  **
        P(bdcGrowthRatePrior.t:Species) = -6.236742222506795 (was -6.236742222506795)
        P(ClockPrior.c:U2SQg5t10r1-2) = -0.9189385332046727 (was -0.9189385332046727)
        P(ClockPrior.c:U2SQg5t10r1-3) = -0.9189385332046727 (was -0.9189385332046727)
        P(ClockPrior.c:U2SQg5t10r1-4) = -0.9189385332046727 (was -0.9189385332046727)
        P(ClockPrior.c:U2SQg5t10r1-5) = -0.9189385332046727 (was -0.9189385332046727)
        P(bdcCollapseWeight.smcTreePrior) = 8.881784197001248E-16 (was 8.881784197001248E-16)
        P(popScalePrior) = 1.1079870517879002 (was 1.1079870517879002)
        P(bdcRelativeDeathRate.smcTreePrior) = 8.881784197001248E-16 (was 8.881784197001248E-16)
    P(likelihood) = NaN (was NaN)  **
        P(treeLikelihood.U2SQg5t10r1-1) = NaN (was NaN)  **
        P(treeLikelihood.U2SQg5t10r1-2) = NaNjava.lang.RuntimeException: Could not find a proper state to initialise. Perhaps try another seed.
See http://www.beast2.org/2018/07/04/fatal-errors.html for other possible solutions.
    at beast.core.MCMC.run(Unknown Source)
    at beast.app.BeastMCMC.run(Unknown Source)
    at beast.app.beastapp.BeastMain.<init>(Unknown Source)
    at beast.app.beastapp.BeastMain.main(Unknown Source)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:64)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:564)
    at beast.app.beastapp.BeastLauncher.run(Unknown Source)
    at beast.app.beastapp.BeastLauncher.main(Unknown Source)
Fatal exception: Could not find a proper state to initialise. Perhaps try another seed.
See http://www.beast2.org/2018/07/04/fatal-errors.html for other possible so (was NaN)  **
        P(treeLikelihood.U2SQg5t10r1-3) = NaN (was NaN)  **
        P(treeLikelihood.U2SQg5t10r1-4) = NaN (was NaN)  **
        P(treeLikelihood.U2SQg5t10r1-5) = NaN (was NaN)  **
Fatal exception: Could not find a proper state to initialise. Perhaps try another seed.
See http://www.beast2.org/2018/07/04/fatal-errors.html for other possible solutions.
lutions.

BEAST has terminated with an error. Please select QUIT from the menu.

I would appreciate your help.

Best regards,

Yanpeng

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