Closed ericenns closed 8 years ago
maxbiostat
commented
8 years ago Hey,
It'd be helpful to know
$ beast -version
ericenns
commented
8 years ago I am using the latest version of BEAST 1.8.3
I am trying to run the xml file provided in the example of the link above.
So this one here, with the sections uncommented as guided by the example.
msuchard
commented
8 years ago @ericenns, try rerun with BEAGLE enabled. If you are still having trouble, please post the entire BEAST screen output.
ericenns
commented
8 years ago Using the following file:
This is the file from the example I had to change lines 953 and 956 to set dimension to 20 instead of 21 as in the example file as that was throwing an error.
With Beagle:
$ java -Djava.library.path=/home/ericenns/lib -jar BEASTv1.8.3/lib/beast.jar H5N1_HA_discrete.xml
BEAST v1.8.3, 2002-2016
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.bio.ed.ac.uk
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 v2.1.2 for accelerated, parallel likelihood evaluation
2009-2013, BEAGLE Working Group - http://beagle-lib.googlecode.com/
Citation: Ayres et al (2012) Systematic Biology 61: 170-173 | doi:10.1093/sysbio/syr100
Random number seed: 1463587958017
Failed to load parser: dr.inferencexml.trace.GeneralizedHarmonicMeanAnalysisParser
line = dr.inferencexml.trace.GeneralizedHarmonicMeanAnalysisParser
Loading additional development parsers from development_parsers.properties, which is additional set of parsers only available for development version ...
WARNING: parser - dr.inferencexml.model.DifferenceParameterParser in development_parsers.properties is duplicated, which is REPLACING the same parser loaded previously.
WARNING: parser - dr.inferencexml.model.SumParameterParser in development_parsers.properties is duplicated, which is REPLACING the same parser loaded previously.
WARNING: parser - dr.evomodelxml.operators.SubtreeJumpOperatorParser in development_parsers.properties is duplicated, which is REPLACING the same parser loaded previously.
Failed to load parser: dr.evomodel.treelikelihood.RootDiscreteStateStatistic
line = dr.evomodel.treelikelihood.RootDiscreteStateStatistic
Failed to load parser: dr.evomodel.epidemiology.casetocase.operators.InfectionBranchGibbsOperator
line = dr.evomodel.epidemiology.casetocase.operators.InfectionBranchGibbsOperator
WARNING: parser - dr.app.beagle.multidimensionalscaling.MultiDimensionalScalingLikelihood in development_parsers.properties is duplicated, which is REPLACING the same parser loaded previously.
Parsing XML file: H5N1_HA_discrete.xml
File encoding: UTF8
Looking for plugins in /home/ericenns/beast_1.8.3_test/plugins
Read alignment: alignment
Sequences = 98
Sites = 1698
Datatype = nucleotide
Site patterns 'patterns' created from positions 1-1698 of alignment 'alignment'
unique pattern count = 464
Read attribute patterns, 'geoPatterns' for attribute, location
Creating Jukes-Cantor distance matrix
Creating the tree model, 'treeModel'
initial tree topology =((((((((((((((((((A_HongKong_486_1997,A_chicken_HongKong_915_1997),A_HongKong_488_1997),A_HongKong_516_1997),A_Duck_HongKong_p46_1997),A_Goose_HongKong_w355_1997),A_HongKong_538_1997),A_HongKong_507_1997),A_HongKong_97_1998),A_HongKong_156_1997),A_HongKong_481_1997),(((((A_HongKong_491_1997,A_HongKong_542_1997),A_HongKong_503_1997),A_Chicken_HongKong_728_1997),A_HongKong_532_1997),(((A_Chicken_HongKong_220_1997,A_chicken_HongKong_258_1997),A_HongKong_483_1997),A_HongKong_485_1997))),A_HongKong_514_1997),((A_duck_Fujian_19_2000,A_duck_Guangdong_12_2000),A_Goose_Guangdong_1_1996)),A_duck_Guangxi_07_1999),((((((((((((A_chicken_Hebei_718_2001,A_duck_Guangxi_35_2001),(A_duck_Fujian_17_2001,A_duck_Guangdong_01_2001)),(A_duck_Guangdong_07_2000,A_duck_Guangdong_40_2000)),A_duck_Guangxi_22_2001),A_duck_Guangdong_22_2002),(A_chicken_Henan_01_2004,A_swine_Fujian_F1_2001)),(((A_blackbird_Hunan_1_2004,A_treesparrow_Henan_4_2004),A_treesparrow_Henan_3_2004),A_treesparrow_Henan_1_2004)),((((A_Ck_HK_619_2002,A_chicken_HongKong_863_2002),A_duck_Guangxi_50_2001),((A_HongKong_213_2003,A_egret_HongKong_7572_2003),A_duck_HongKong_821_2002)),((A_chicken_jiyuan_1_2003,A_chicken_zhengzhou_1_2002),A_chicken_Guangdong_174_2004))),A_duck_Shantou_4610_2003),((((A_duck_Fujian_01_2002,A_duck_Fujian_13_2002),A_chicken_Hebei_108_2002),A_chicken_zhoukou_2_2002),A_duck_Guangxi_53_2002)),(((A_chicken_Fujian_1042_2005,A_duck_Fujian_897_2005),A_Goose_Shantou_1621_2005),A_goose_Shantou_2216_2005)),A_duck_Guangdong_173_2004)),(A_chicken_Hebei_326_2005,A_treesparrow_Henan_2_2004)),(((((((((A_duck_Guangxi_351_2004,A_duck_Guangxi_380_2004),A_chicken_Guangdong_178_2004),(A_greyheron_HongKong_728_2004,A_greyheron_HongKong_837_2004)),((A_chicken_Guangxi_604_2005,A_duck_Guangxi_793_2005),A_quail_Guangxi_575_2005)),(((A_chicken_Guangxi_2448_2004,A_chicken_Guangxi_2461_2004),(A_duck_Hunan_1265_2005,A_duck_Hunan_1608_2005)),(A_duck_Guangxi_951_2005,A_goose_Guangxi_345_2005))),(A_Chicken_Shantou_810_2005,A_Quail_Shantou_911_2005)),A_chicken_Guangdong_191_2004),A_Duck_Fujian_1734_2005),((((A_chicken_Hunan_999_2005,A_duck_Hunan_182_2005),A_duck_Hunan_139_2005),(A_duck_Hunan_127_2005,A_duck_Hunan_152_2005)),A_duck_Hunan_157_2005))),(((((((((A_duck_Guangxi_1586_2004,A_duck_Guangxi_1681_2004),A_duck_Guangxi_1311_2004),A_duck_Guangxi_1793_2004),(A_goose_Guangxi_1097_2004,A_goose_Guangxi_1832_2004)),A_goose_Guangxi_2112_2004),(A_duck_Guangxi_2396_2004,A_goose_Guangxi_2383_2004)),A_duck_Guangxi_2291_2004),A_chicken_Gu angxi_2439_2004),(A_duck_
Guangxi_1378_2004,A_goose_Guangxi_914_2004)))
tree height = 9.00012400328392
Using discretized relaxed clock model.
over sampling = 1
parametric model = logNormalDistributionModel
rate categories = 194
Creating state frequencies model 'hky.frequencies': Using empirical frequencies from data = {0.34814, 0.18686, 0.22972, 0.23528}
Creating HKY substitution model. Initial kappa = 1.0
Creating site model:
4 category discrete gamma with initial shape = 0.5
Using BEAGLE TreeLikelihood
Branch rate model used: discretizedBranchRates
Using BEAGLE resource 0: CPU
with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU
Ignoring ambiguities in tree likelihood.
With 464 unique site patterns.
Using rescaling scheme : dynamic (rescaling every 100 evaluations)
Creating state frequencies model 'geoFreqs.frequencies': Initial frequencies = {0.14286, 0.14286, 0.14286, 0.14286, 0.14286, 0.14286, 0.14286}
General Substitution Model (stateCount=7)
Rates relative to Fujian<->Guangdong
Fatal exception: Length of dimension name array doesn't match the number of dimensions
java.lang.IllegalArgumentException: Length of dimension name array doesn't match the number of dimensions
at dr.inference.model.Parameter$Abstract.setDimensionNames(Unknown Source)
at dr.app.beagle.evomodel.substmodel.GeneralSubstitutionModel.setupDimensionNames(Unknown Source)
at dr.app.beagle.evomodel.substmodel.GeneralSubstitutionModel.<init>(Unknown Source)
at dr.app.beagle.evomodel.substmodel.GeneralSubstitutionModel.<init>(Unknown Source)
at dr.app.beagle.evomodel.parsers.GeneralSubstitutionModelParser.parseXMLObject(Unknown Source)
at dr.xml.AbstractXMLObjectParser.parseXMLObject(Unknown Source)
at dr.xml.XMLParser.convert(Unknown Source)
at dr.xml.XMLParser.convert(Unknown Source)
at dr.xml.XMLParser.parse(Unknown Source)
at dr.app.beast.BeastMain.<init>(Unknown Source)
at dr.app.beast.BeastMain.main(Unknown Source)
java.lang.RuntimeException: Terminate
at dr.app.beast.BeastMain.<init>(Unknown Source)
at dr.app.beast.BeastMain.main(Unknown Source)Without Beagle:
$ java -jar BEASTv1.8.3/lib/beast.jar -beagle_off H5N1_HA_discrete.xml
BEAST v1.8.3, 2002-2016
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.bio.ed.ac.uk
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
Random number seed: 1463588388373
Failed to load parser: dr.inferencexml.trace.GeneralizedHarmonicMeanAnalysisParser
line = dr.inferencexml.trace.GeneralizedHarmonicMeanAnalysisParser
Loading additional development parsers from development_parsers.properties, which is additional set of parsers only available for development version ...
WARNING: parser - dr.inferencexml.model.DifferenceParameterParser in development_parsers.properties is duplicated, which is REPLACING the same parser loaded previously.
WARNING: parser - dr.inferencexml.model.SumParameterParser in development_parsers.properties is duplicated, which is REPLACING the same parser loaded previously.
WARNING: parser - dr.evomodelxml.operators.SubtreeJumpOperatorParser in development_parsers.properties is duplicated, which is REPLACING the same parser loaded previously.
Failed to load parser: dr.evomodel.treelikelihood.RootDiscreteStateStatistic
line = dr.evomodel.treelikelihood.RootDiscreteStateStatistic
Failed to load parser: dr.evomodel.epidemiology.casetocase.operators.InfectionBranchGibbsOperator
line = dr.evomodel.epidemiology.casetocase.operators.InfectionBranchGibbsOperator
WARNING: parser - dr.app.beagle.multidimensionalscaling.MultiDimensionalScalingLikelihood in development_parsers.properties is duplicated, which is REPLACING the same parser loaded previously.
Parsing XML file: H5N1_HA_discrete.xml
File encoding: UTF8
Looking for plugins in /home/ericenns/beast_1.8.3_test/plugins
Read alignment: alignment
Sequences = 98
Sites = 1698
Datatype = nucleotide
Site patterns 'patterns' created from positions 1-1698 of alignment 'alignment'
unique pattern count = 464
Read attribute patterns, 'geoPatterns' for attribute, location
Creating Jukes-Cantor distance matrix
Creating the tree model, 'treeModel'
initial tree topology = ((((((((((((((((((A_HongKong_486_1997,A_chicken_HongKong_915_1997),A_HongKong_488_1997),A_HongKong_516_1997),A_Duck_HongKong_p46_1997),A_Goose_HongKong_w355_1997),A_HongKong_538_1997),A_HongKong_507_1997),A_HongKong_97_1998),A_HongKong_156_1997),A_HongKong_481_1997),(((((A_HongKong_491_1997,A_HongKong_542_1997),A_HongKong_503_1997),A_Chicken_HongKong_728_1997),A_HongKong_532_1997),(((A_Chicken_HongKong_220_1997,A_chicken_HongKong_258_1997),A_HongKong_483_1997),A_HongKong_485_1997))),A_HongKong_514_1997),((A_duck_Fujian_19_2000,A_duck_Guangdong_12_2000),A_Goose_Guangdong_1_1996)),A_duck_Guangxi_07_1999),((((((((((((A_chicken_Hebei_718_2001,A_duck_Guangxi_35_2001),(A_duck_Fujian_17_2001,A_duck_Guangdong_01_2001)),(A_duck_Guangdong_07_2000,A_duck_Guangdong_40_2000)),A_duck_Guangxi_22_2001),A_duck_Guangdong_22_2002),(A_chicken_Henan_01_2004,A_swine_Fujian_F1_2001)),(((A_blackbird_Hunan_1_2004,A_treesparrow_Henan_4_2004),A_treesparrow_Henan_3_2004),A_treesparrow_Henan_1_2004)),((((A_Ck_HK_619_2002,A_chicken_HongKong_863_2002),A_duck_Guangxi_50_2001),((A_HongKong_213_2003,A_egret_HongKong_7572_2003),A_duck_HongKong_821_2002)),((A_chicken_jiyuan_1_2003,A_chicken_zhengzhou_1_2002),A_chicken_Guangdong_174_2004))),A_duck_Shantou_4610_2003),((((A_duck_Fujian_01_2002,A_duck_Fujian_13_2002),A_chicken_Hebei_108_2002),A_chicken_zhoukou_2_2002),A_duck_Guangxi_53_2002)),(((A_chicken_Fujian_1042_2005,A_duck_Fujian_897_2005),A_Goose_Shantou_1621_2005),A_goose_Shantou_2216_2005)),A_duck_Guangdong_173_2004)),(A_chicken_Hebei_326_2005,A_treesparrow_Henan_2_2004)),(((((((((A_duck_Guangxi_351_2004,A_duck_Guangxi_380_2004),A_chicken_Guangdong_178_2004),(A_greyheron_HongKong_728_2004,A_greyheron_HongKong_837_2004)),((A_chicken_Guangxi_604_2005,A_duck_Guangxi_793_2005),A_quail_Guangxi_575_2005)),(((A_chicken_Guangxi_2448_2004,A_chicken_Guangxi_2461_2004),(A_duck_Hunan_1265_2005,A_duck_Hunan_1608_2005)),(A_duck_Guangxi_951_2005,A_goose_Guangxi_345_2005))),(A_Chicken_Shantou_810_2005,A_Quail_Shantou_911_2005)),A_chicken_Guangdong_191_2004),A_Duck_Fujian_1734_2005),((((A_chicken_Hunan_999_2005,A_duck_Hunan_182_2005),A_duck_Hunan_139_2005),(A_duck_Hunan_127_2005,A_duck_Hunan_152_2005)),A_duck_Hunan_157_2005))),(((((((((A_duck_Guangxi_1586_2004,A_duck_Guangxi_1681_2004),A_duck_Guangxi_1311_2004),A_duck_Guangxi_1793_2004),(A_goose_Guangxi_1097_2004,A_goose_Guangxi_1832_2004)),A_goose_Guangxi_2112_2004),(A_duck_Guangxi_2396_2004,A_goose_Guangxi_2383_2004)),A_duck_Guangxi_2291_2004),A_chicken_Guangxi_2439_2004),(A_duck_Guangxi_1378_2004,A_goose_Guangxi_914_2004)))
tree height = 9.000049988483193
Using discretized relaxed clock model.
over sampling = 1
parametric model = logNormalDistributionModel
rate categories = 194
Creating state frequencies model 'hky.frequencies': Using empirical frequencies from data = {0.34814, 0.18686, 0.22972, 0.23528}
Creating HKY substitution model. Initial kappa = 1.0
Creating site model.
4 category discrete gamma with initial shape = 0.5
Failed to load native NucleotideLikelihoodCore in : /home/ericenns/beast_1.8.3_test
Using Java nucleotide likelihood core because java.lang.UnsatisfiedLinkError: no NucleotideLikelihoodCore in java.library.path
TreeLikelihood(treeModel) using Java nucleotide likelihood core
Ignoring ambiguities in tree likelihood.
With 464 unique site patterns.
Branch rate model used: discretizedBranchRates
Creating state frequencies model 'geoFreqs.frequencies': Initial frequencies = {0.14286, 0.14286, 0.14286, 0.14286, 0.14286, 0.14286, 0.14286}
General Substitution Model (stateCount=7)
Rates relative to Fujian<->Guangdong
Creating site model.
with initial substitution rate = 0.1
Creating swap operator for parameter branchRates.categories (weight=30.0)
dr.xml.XMLParseException: The '<bitFlipInSubstitutionModelOperator>' element with id, 'null', is incorrectly constructed.
The following was expected:
Exactly one ELEMENT of type BayesianStochasticSearchVariableSelection REQUIRED
at dr.xml.AbstractXMLObjectParser.parseXMLObject(Unknown Source)
at dr.xml.XMLParser.convert(Unknown Source)
at dr.xml.XMLParser.convert(Unknown Source)
at dr.xml.XMLParser.convert(Unknown Source)
at dr.xml.XMLParser.parse(Unknown Source)
at dr.app.beast.BeastMain.<init>(Unknown Source)
at dr.app.beast.BeastMain.main(Unknown Source)
May 18, 2016 11:19:49 AM dr.app.beast.BeastMain <init>
SEVERE: Parsing error - poorly formed BEAST file, H5N1_HA_discrete.xml:
The '<bitFlipInSubstitutionModelOperator>' element with id, 'null', is incorrectly constructed.
The following was expected:
Exactly one ELEMENT of type BayesianStochasticSearchVariableSelection REQUIRED
java.lang.RuntimeException: Terminate
at dr.app.beast.BeastMain.<init>(Unknown Source)
at dr.app.beast.BeastMain.main(Unknown Source)
rambaut
commented
8 years ago The tutorial is out of date. This can be setup from within BEAUti.
I have tried following the BSSVS example available here
And I get the following errors:
Any advice: