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expansion model numerical integration #36

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1.
2.
3.

What is the expected output? What do you see instead?

Attached file should run properly.

Please use labels and text to provide additional information.

User report 

> From: Siobain Duffy <smd16@psu.edu>
> Date: 17 September 2007 10:17:35 PM
> To: alexei@cs.auckland.ac.nz
> Cc: a.rambaut@ed.ac.uk
> Subject: Beast 1.4.4 severe error, too many iterations in
getNumericalIntegral
>
> Hello,
>
> Thank you so much for creating and maintaining BEAST!
>
> A run this morning failed and told me to inform you, so here's the log
file, the xml file, and the text of the log file also follows this email.
>
> It is a relaxed (exponential) molecular clock/expansion demographic model
.xml file, which was created with BEAUTI 1.4.4.
>
> Thank you, and please contact me if you need any additional information,
> Siobain Duffy
>
> NSF Postdoctoral Fellow
> Center for Infectious Disease Dynamics
> The Pennsylvania State University
>
>
>
>
>                   BEAST v1.4.4, 2002-2007
>        Bayesian Evolutionary Analysis Sampling Trees
>                              by
>            Alexei J. Drummond and Andrew Rambaut
>
>                Department of Computer Science
>                    University of Auckland
>                   alexei@cs.auckland.ac.nz
>
>              Institute of Evolutionary Biology
>                   University of Edinburgh
>                      a.rambaut@ed.ac.uk
>
> Downloads, Help & Resources:
> http://beast.bio.ed.ac.uk/
>
> Source code distributed under the GNU Lesser General Public License:
> http://code.google.com/p/beast-mcmc/
>
> Additional programming & components created by:
> Roald Forsberg
> Gerton Lunter
> Sidney Markowitz
> Oliver Pybus
>
> Thanks to (for use of their code):
> Korbinian Strimmer
>
> Random number seed: 1190022893839
>
> MacRoman
> Parsing XML file: Bv1EXPexpand
> Read alignment, 'alignment':
>   Sequences = 43
>       Sites = 798
>    Datatype = nucleotide
> Site patterns 'patterns' created from positions 1-798 of alignment
'alignment'
>   pattern count = 177
> Creating the tree model, 'treeModel'
>   initial tree topology =
((((((((((EACMV-K35,EACMV-UGK140),EACMZV-K10),EACMV-UG3Svr),(EACMV-K29,EACMV-UG3
Mld)),((EACMV-K211,EACMV-UG1),EACMV-UGK115)),(((EACMV-K24,EACMZV-K270),(EACMV-KE
2K25,EACMV-UGK282)),EACMKV-K300)),((((EACMV-UGK81,EACMZV-K212),EACMKV-K228),EACM
ZV-K272),((EACMKV-K230,EACMKV-K261),EACMV-UGK223))),(((EACMZV-K18,EACMZV-K275),E
ACMV-KE2K208),EACMZV-K19)),(((((((EACMV-UGK137,EACMV-UGK66),(EACMV-UGK72,EACMZV-
K3)),EACMV-UGK23),EACMV-KE2K27),EACMKV-K238),EACMV-KE2K48),(EACMKV-K229,EACMV-K3
25))),(((((EACMV-KEK197,EACMV-UGK262),EACMV-UGK90),EACMV-UGK79),EACMV-K268),((EA
CMV-KE2K201,EACMZV-KE:Kil),EACMZV-K337)))
> Using discretized relaxed clock model.
>   parametric model = exponentialDistributionModel
>    rate categories = 84
> Creating site model:
>   4 category discrete gamma with initial shape = 0.5
>   initial proportion of invariant sites = 0.5
> TreeLikelihood using native nucleotide likelihood core
>   Ignoring ambiguities in tree likelihood.
>   Partial likelihood scaling off.
> Branch rate model used: discretizedBranchRates
> Creating swap operator for parameter branchRates.categories (weight=30)
> Creating the MCMC chain:
>   chainLength=10000000
>   autoOptimize=true
>   fullEvaluation=2000
> Sep 17, 2007 6:07:35 AM dr.app.beast.BeastMain <init>
> SEVERE: Error running file: Bv1EXPexpand
> Sep 17, 2007 6:07:35 AM dr.app.beast.BeastMain <init>
> SEVERE: Fatal exception (email the authors)
> Fatal exception (email the authors)
> java.lang.RuntimeException: Too many iterations in getNumericalIntegral
> at
dr.evolution.coalescent.DemographicFunction$Abstract.getNumericalIntegral(Unknow
n
Source)
> at dr.evolution.coalescent.Expansion.getIntegral(Unknown Source)
> at dr.evolution.coalescent.Coalescent.calculateLogLikelihood(Unknown Source)
> at
dr.evomodel.coalescent.NewCoalescentLikelihood.calculateLogLikelihood(Unknown
Source)
> at
dr.evomodel.coalescent.NewCoalescentLikelihood.getLogLikelihood(Unknown Source)
> at dr.inference.model.CompoundLikelihood.getLogLikelihood(Unknown Source)
> at dr.inference.model.CompoundLikelihood.getLogLikelihood(Unknown Source)
> at dr.inference.markovchain.MarkovChain.evaluate(Unknown Source)
> at dr.inference.markovchain.MarkovChain.<init>(Unknown Source)
> at dr.inference.mcmc.MCMC.init(Unknown Source)
> at dr.inference.mcmc.MCMC$2.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)
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
> at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.jav
a:25)
> at java.lang.reflect.Method.invoke(Method.java:585)
> at apple.launcher.LaunchRunner.run(LaunchRunner.java:88)
> at apple.launcher.LaunchRunner.callMain(LaunchRunner.java:50)
> at
apple.launcher.JavaApplicationLauncher.launch(JavaApplicationLauncher.java:52)
>
>
>
>
>

Original issue reported on code.google.com by jhe...@gmail.com on 13 Nov 2007 at 11:03

Attachments:

GoogleCodeExporter commented 9 years ago 
Checked in the fix (1.4 branch)

Original comment by jhe...@gmail.com on 14 Nov 2007 at 3:20

GoogleCodeExporter commented 9 years ago

Original comment by ramb...@gmail.com on 31 Jan 2008 at 10:18