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

[Nick Matzke]

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:

http://phylo.wikidot.com/local--files/beastmaster/ITS_continuous_phylogeog_1trait.xml

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:

http://phylo.wdfiles.com/local--files/beastmaster/TreeTraitMap_validate_null_error2.xml

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]

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

[Nick Matzke]

Thanks Remco,

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

Cheers, Nick

--
You received this message because you are subscribed to the Google Groups "beast-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to beast-users...@googlegroups.com.
To post to this group, send email to beast...@googlegroups.com.
Visit this group at http://groups.google.com/group/beast-users.
For more options, visit https://groups.google.com/d/optout.

--
You received this message because you are subscribed to the Google Groups "beast-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to beast-users...@googlegroups.com.
To post to this group, send email to beast...@googlegroups.com.
Visit this group at http://groups.google.com/group/beast-users.
For more options, visit https://groups.google.com/d/optout.

--
You received this message because you are subscribed to the Google Groups "beast-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to beast-users...@googlegroups.com.
To post to this group, send email to beast...@googlegroups.com.
Visit this group at http://groups.google.com/group/beast-users.
For more options, visit https://groups.google.com/d/optout.