Hi all (especially Remco),
I've been tearing my hair out for hours attempting to figure out this issue, I figured it would be worth seeing if someone has a thought about it.
I would like include a single continuous trait in an analysis. Here is a working XML file (modified from a Beast example) that does this successfully:
Works:
In this file (cut waaaay down to make it a small example of the problem), I tried to replicate every feature of the continuous trait data and model. After a million attempts at varying just about every option I still get the same error. So perhaps it's something simple that I'm missing.
Doesn't work:
Here's the error message. It's something about specifying the trait values. Any help VERY APPRECIATED!!
Thanks,
Nick
===========================
java -Xms512m -Xmx512m -jar /Applications/BEAST_2.1.3/lib/beast.jar -java -seed 754321 -overwrite TreeTraitMap_validate_null_error2.xml
BEAST v2.1.3, 2002-2014
Bayesian Evolutionary Analysis Sampling Trees
Designed and developed by
Remco Bouckaert, Alexei J. Drummond, Andrew Rambaut and Marc A. Suchard
Department of Computer Science
University of Auckland
Institute of Evolutionary Biology
University of Edinburgh
David Geffen School of Medicine
University of California, Los Angeles
Downloads, Help & Resources:
Source code distributed under the GNU Lesser General Public License:
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: 754321
File: TreeTraitMap_validate_null_error2.xml seed: 754321 threads: 1
Probing: BDSSM.addon.jar Loaded URL file:/Users/matzke/Library/Application Support/BEAST/2.1/BDSKY/lib/BDSSM.addon.jar
Probing: BEAST_CLASSIC.addon.jar Loaded URL file:/Users/matzke/Library/Application Support/BEAST/2.1/BEAST_CLASSIC/lib/BEAST_CLASSIC.addon.jar
Probing: BEASTlabs.addon.jar Loaded URL file:/Users/matzke/Library/Application Support/BEAST/2.1/BEASTlabs/lib/BEASTlabs.addon.jar
Probing: DISSECT.jar Loaded URL file:/Users/matzke/Library/Application Support/BEAST/2.1/DISSECT/lib/DISSECT.jar
Probing: antlr-runtime-4.2.jar Loaded URL file:/Users/matzke/Library/Application Support/BEAST/2.1/MASTER/lib/antlr-runtime-4.2.jar
Probing: guava-16.0.1.jar Loaded URL file:/Users/matzke/Library/Application Support/BEAST/2.1/MASTER/lib/guava-16.0.1.jar
Probing: jackson-annotations-2.2.3.jar Loaded URL file:/Users/matzke/Library/Application Support/BEAST/2.1/MASTER/lib/jackson-annotations-2.2.3.jar
Probing: jackson-core-2.2.3.jar Loaded URL file:/Users/matzke/Library/Application Support/BEAST/2.1/MASTER/lib/jackson-core-2.2.3.jar
Probing: jackson-databind-2.2.3.jar Loaded URL file:/Users/matzke/Library/Application Support/BEAST/2.1/MASTER/lib/jackson-databind-2.2.3.jar
Probing: MASTER.package.v1.6.0.jar Loaded URL file:/Users/matzke/Library/Application Support/BEAST/2.1/MASTER/lib/MASTER.package.v1.6.0.jar
Probing: MODEL_SELECTION.addon.jar Loaded URL file:/Users/matzke/Library/Application Support/BEAST/2.1/MODEL_SELECTION/lib/MODEL_SELECTION.addon.jar
Probing: guava-15.0.jar Skip loading file:/Users/matzke/Library/Application Support/BEAST/2.1/MultiTypeTree/lib/guava-15.0.jar: contains classs com.google.common.annotations.Beta that is already loaded
Probing: jblas-1.2.3.jar Loaded URL file:/Users/matzke/Library/Application Support/BEAST/2.1/MultiTypeTree/lib/jblas-1.2.3.jar
Probing: MultiTypeTree.v2.0.1.jar Skip loading file:/Users/matzke/Library/Application Support/BEAST/2.1/MultiTypeTree/lib/MultiTypeTree.v2.0.1.jar: contains classs beast.math.distributions.ExcludablePrior that is already loaded
Probing: phylodynamics.addon.jar Loaded URL file:/Users/matzke/Library/Application Support/BEAST/2.1/phylodynamics/lib/phylodynamics.addon.jar
Probing: RBS.addon.jar Loaded URL file:/Users/matzke/Library/Application Support/BEAST/2.1/RBS/lib/RBS.addon.jar
Probing: SA.addon.jar Loaded URL file:/Users/matzke/Library/Application Support/BEAST/2.1/SA/lib/SA.addon.jar
Probing: snap.addon.jar Loaded URL file:/Users/matzke/Library/Application Support/BEAST/2.1/SNAPP/lib/snap.addon.jar
Probing: colt.jar Skip loading file:/Users/matzke/Library/Application Support/BEAST/2.1/SubstBMA/lib/colt.jar: contains classs cern.clhep.PhysicalConstants that is already loaded
Probing: SubstBMA.addon.jar Loaded URL file:/Users/matzke/Library/Application Support/BEAST/2.1/SubstBMA/lib/SubstBMA.addon.jar
SiteModel => beast.evolution.sitemodel.SiteModel
Beta => beast.math.distributions.Beta
Exponential => beast.math.distributions.Exponential
InverseGamma => beast.math.distributions.InverseGamma
LogNormal => beast.math.distributions.LogNormalDistributionModel
Gamma => beast.math.distributions.Gamma
Uniform => beast.math.distributions.Uniform
prior => beast.math.distributions.Prior
LaplaceDistribution => beast.math.distributions.LaplaceDistribution
OneOnX => beast.math.distributions.OneOnX
Normal => beast.math.distributions.Normal
Element parameter found with idref='morph_relRate'. All other attributes are ignored.
Element parameter found with idref='ucldMean_of_shared_clock'. All other attributes are ignored.
Element tree found with idref='shared_tree'. All other attributes are ignored.
Element parameter found with idref='ucldMean_of_shared_clock'. All other attributes are ignored.
Element parameter found with idref='ucldStdev_of_shared_clock'. All other attributes are ignored.
Element parameter found with idref='morph_relRate'. All other attributes are ignored.
Element parameter found with idref='ucldMean_of_shared_clock'. All other attributes are ignored.
Element parameter found with idref='morph_relRate'. All other attributes are ignored.
taxon22: 264 2
Pan_troglodytes: 264 2
taxon21: 264 2
taxon20: 264 2
taxon19: 264 2
taxon18: 264 2
taxon17: 264 2
taxon16: 264 2
taxon15: 264 2
taxon14: 264 2
taxon13: 264 2
taxon12: 264 2
taxon11: 264 2
13 taxa
264 sites
161 patterns
java.lang.NullPointerException
at beast.evolution.tree.TreeTraitMap.initAndValidate(Unknown Source)
at beast.util.XMLParser.initPlugins(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)
Error 110 parsing the xml input file
validate and intialize error: null
Error detected about here:
<beast>
<run id='mcmc' spec='MCMC'>
<distribution id='posterior' spec='util.CompoundDistribution'>
<distribution id='prior' spec='util.CompoundDistribution'>
<prior id='Prior_on_traits_table_trait1_rootTrait' name='distribution'>
<x id='traits_table_trait1_rootTrait' spec='beast.evolution.tree.RootTrait'>
<traitmap id='traitmap1' spec='beast.evolution.tree.TreeTraitMap'>
===========================