TraitMap problem: Error 110 parsing the xml input file validate and intialize error: null

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Nick Matzke

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Mar 15, 2015, 2:35:30 AM3/15/15
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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
                  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.cs.auckland.ac.nz
                              
Source code distributed under the GNU Lesser General Public License:
              http://code.google.com/p/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: 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'>

===========================

Remco Bouckaert

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Mar 15, 2015, 3:49:39 PM3/15/15
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Hi Nick,

The problem is caused by the order in which objects are initialised — the triatmap became initialised earlier than the tree’s taxonset causing the null pointer exception. One way to solve this is by having a tree and a separate initialiser. I massaged the XML you posted a bit and got something that runs. Where I changed it, I added a commend starting with RRB. Note I also needed to add a clock model, and added a strict clock with rate 1, just so the XML runs now.

This solution is a bit more magical than I would like it to be, so I raised an issue to have a closer look at this.

Cheers,

Remco



p2.xml

Nick Matzke

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Mar 15, 2015, 4:37:45 PM3/15/15
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Thanks Remco,

It runs for me also now.  Thanks, you're a lifesaver!!

Cheers, Nick


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