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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