GRMF Skyride example xml non-functional in BEAST2 v.2.5

[David Pascall]

I've been trying to set up a Skyride analysis in version 2.5.0. Skyrides can't be set up through beauti (as far as I can tell, so I've been attempting to canibalise the example XML linked here: http://www.beast2.org/beast-features/). I couldn't for the life of me get it to work, and I couldn't work out why. Then I tried to just run the example XML (which probably should have been the first thing I did) and it itself errored out. I have beast-classic installed, so I'm stuck as to what else it could be, unless the syntax has changed slightly since it was written.

Any help pointing to what needs to be changed so that it will run (and I can steal the lines for my analysis) would be greatly appreciated.

Here's the error message:

---

./beast -working /Users/XXX/Desktop/skyride.xml
[java, -Djava.library.path=/Users/XXX/Library/Java/Extensions:/Library/Java/Extensions:/Network/Library/Java/Extensions:/System/Library/Java/Extensions:/usr/lib/java:/Applications/BEAST 2.5.0/bin/., -cp, ::/Users/XXX/Library/Application Support/BEAST/2.5/BEAST/lib/beast.src.jar:/Users/XXX/Library/Application Support/BEAST/2.5/BEAST/lib/beast.jar:/Users/XXX/Library/Application Support/BEAST/2.5/bModelTest/lib/bModelTest.addon.jar:/Users/XXX/Library/Application Support/BEAST/2.5/GEO_SPHERE/lib/jts-1.8.jar:/Users/XXX/Library/Application Support/BEAST/2.5/GEO_SPHERE/lib/jump-core-1.2.jar:/Users/XXX/Library/Application Support/BEAST/2.5/GEO_SPHERE/lib/GEO.addon.jar:/Users/XXX/Library/Application Support/BEAST/2.5/GEO_SPHERE/lib/Jama-1.0.1.jar:/Users/XXX/Library/Application Support/BEAST/2.5/GEO_SPHERE/lib/jump-workbench-1.2.jar:/Users/XXX/Library/Application Support/BEAST/2.5/GEO_SPHERE/lib/xerces.jar:/Users/XXX/Library/Application Support/BEAST/2.5/GEO_SPHERE/lib/jdom.jar:/Users/XXX/Library/Application Support/BEAST/2.5/MASTER/lib/jackson-databind-2.2.3.jar:/Users/XXX/Library/Application Support/BEAST/2.5/MASTER/lib/jackson-core-2.2.3.jar:/Users/XXX/Library/Application Support/BEAST/2.5/MASTER/lib/MASTER.package.v6.0.0.jar:/Users/XXX/Library/Application Support/BEAST/2.5/MASTER/lib/guava-16.0.1.jar:/Users/XXX/Library/Application Support/BEAST/2.5/MASTER/lib/jackson-annotations-2.2.3.jar:/Users/XXX/Library/Application Support/BEAST/2.5/BEASTLabs/lib/BEASTlabs.addon.jar:/Users/XXX/Library/Application Support/BEAST/2.5/BEAST_CLASSIC/lib/BEAST_CLASSIC.addon.jar:/Users/XXX/Library/Application Support/BEAST/2.5/BEAST_CLASSIC/lib/mtj.jar:/Applications/BEAST 2.5.0/lib/launcher.jar:/Applications/BEAST 2.5.0/lib/beast.src.jar:/Applications/BEAST 2.5.0/lib/beast.jar, beast.app.beastapp.BeastMain, -working, /Users/XXX/Desktop/skyride.xml]

                        BEAST v2.5.0, 2002-2018
             Bayesian Evolutionary Analysis Sampling Trees
                       Designed and developed by
 Remco Bouckaert, Alexei J. Drummond, Andrew Rambaut & 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.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: 1531212310924

File: skyride.xml seed: 1531212310924 threads: 1
Alignment(x)
  33 taxa
  1879 sites
  173 patterns

W2P1D0 = 0.0 (54.0)
W2P12D0 = 0.0 (54.0)
W2P4D5 = 5.0 (49.0)
W2P8D5 = 5.0 (49.0)
W2P9D5 = 5.0 (49.0)
W2P1D12 = 12.0 (42.0)
W2P2D12 = 12.0 (42.0)
W2P15D12 = 12.0 (42.0)
W2P1D18 = 18.0 (36.0)
W2P2D18 = 18.0 (36.0)
W2P3D18 = 18.0 (36.0)
W2P4D18 = 18.0 (36.0)
W2P1D30 = 30.0 (24.0)
W2P2D30 = 30.0 (24.0)
W2P3D30 = 30.0 (24.0)
W2P4D30 = 30.0 (24.0)
W2P5D30 = 30.0 (24.0)
W2P6D30 = 30.0 (24.0)
W2P7D30 = 30.0 (24.0)
W2P1D34 = 34.0 (20.0)
W2P2D34 = 34.0 (20.0)
W2P5D34 = 34.0 (20.0)
W2P14D34 = 34.0 (20.0)
W2P1D36 = 36.0 (18.0)
W2P12D36 = 36.0 (18.0)
W2P1D41 = 41.0 (13.0)
W2P2D41 = 41.0 (13.0)
W2P5D41 = 41.0 (13.0)
W2P7D41 = 41.0 (13.0)
W2P9D41 = 41.0 (13.0)
W2P1D48 = 48.0 (6.0)
W2P1D54 = 54.0 (0.0)
W2P7D54 = 54.0 (0.0)
java.lang.NullPointerException
    at beast.evolution.tree.coalescent.GMRFSkyrideLikelihood.getCorrectFieldLength(Unknown Source)
    at beast.evolution.tree.coalescent.GMRFSkyrideLikelihood.initAndValidate(Unknown Source)
    at beast.util.XMLParser.initBEASTObjects(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'>
                  <distribution id='skyride' spec='beast.evolution.tree.coalescent.GMRFSkyrideLikelihood'>

java.lang.UNIXProcess$ProcessPipeInputStream@b1bc7ed

[Koenievdl]

I'm experiencing the same issue. Since I switched to beast2 v2.5.0 my runs crash with the error message:

 java.lang.UNIXProcess$ProcessPipeInputStream@4fca772d

[Tim Vaughan]

Hi Koenievdl, is your crash also related to the GMRF skyride model in
beast 2? The line at the end is common to many beast 2 crash reports
and unfortunately isn't enough to identify what's going wrong.

In case your error is in fact to do with the GMRF skyride, this is due
to an error in the example XML (discussion here:
https://github.com/BEAST2-Dev/beast-classic/issues/6). This has now
been fixed and the test XML should once again work.

All the best,

Tim

On Thu, 20 Sep 2018 at 11:16, Koenievdl <koenvand...@hotmail.com> wrote:
>
> I'm experiencing the same issue. Since I switched to beast2 v2.5.0 my runs crash with the error message:
> java.lang.UNIXProcess$ProcessPipeInputStream@4fca772d
>

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[Joseph Hicks]

When trying to run a GMRF Skyride model in BEAST2 on my own data, I noticed the skyrideLogPopSize parameters remained constant throughout the MCMC. Assuming I adapted my xml file incorrectly, I ran the testSkyRide.xml file from the github page and the same thing occurred. Using BEAST 1.10 on my data, the LogPopSize seems to be sampled just fine. Any help on why those parameters would stay at the initial value for the whole MCMC run in BEAST2?

Thanks,

--Joe