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Bayesian Evolutionary Analysis Sampling Trees
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BEAUti 1.6.1 sequenceErrorModel xml not work in BEAST #445

Closed msuchard closed 9 years ago

msuchard commented 9 years ago

Originally reported on Google Code with ID 436

Dear Everybody:

      Enclosed is my XML file, which is created by BEAUti 1.6.1. But this file can
not run in BEAST 1.6.1., I don't know why, would you please help me check it?

     Cheers,

     Rong

Rong Li, Ph.D. 
Key Laboratory of Biodiversity and Biogeography, 
Kunming Institute of Botany, 
Chinese Academy of Sciences, 
132 #, Lanhei Road, Heilongtan, 
Kunming 650204, Yunnan Province, 
P. R. of China 
E-mail: lirong@mail.kib.ac.cn 
              lirong_welcome@yahoo.com 
              lirong_welcome@hotmail.com

Reported by dong.w.xie on 2010-12-01 04:58:32

msuchard commented 9 years ago 
Bug in TipPartialsModel used for sequenceErrorModel 

Branch rate model used: discretizedBranchRates
Error running file: combined.xml
Fatal exception: null

java.lang.NullPointerException
    at dr.evolution.alignment.SitePatterns.getPatternState(SitePatterns.java:432)
    at dr.evomodel.treelikelihood.TipPartialsModel.setStates(TipPartialsModel.java:96)
    at dr.evomodel.treelikelihood.TreeLikelihood.<init>(TreeLikelihood.java:165)
    at dr.evomodelxml.treelikelihood.TreeLikelihoodParser.parseXMLObject(TreeLikelihoodParser.java:50)
    at dr.xml.AbstractXMLObjectParser.parseXMLObject(AbstractXMLObjectParser.java:120)
    at dr.xml.XMLParser.convert(XMLParser.java:289)
    at dr.xml.XMLParser.convert(XMLParser.java:260)
    at dr.xml.XMLParser.parse(XMLParser.java:163)
    at dr.app.beast.BeastMain.<init>(BeastMain.java:148)
    at dr.app.beast.BeastMain.main(BeastMain.java:533)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
    at java.lang.reflect.Method.invoke(Method.java:585)
    at com.intellij.rt.execution.application.AppMain.main(AppMain.java:90)

Reported by dong.w.xie on 2010-12-09 22:06:45

msuchard commented 9 years ago

Reported by dong.w.xie on 2011-02-17 21:31:34

msuchard commented 9 years ago 
The reason this is happening is that the same SequenceErrorModel is being used for all
the TreeLikelihoods for this multi partition analysis.

Reported by rambaut on 2011-04-20 07:45:54

msuchard commented 9 years ago 
Fixed this by disabling the Sequence Error Model option in BEAUti if there is more than
one partition. This is not the ideal solution but prevents non-working XML being generated.
To get the XML, above working, the SequenceErrorModel would have to be duplicated to
have one per TreeLikelihood (they could share the same parameter and thus be jointly
estimated).

Reported by rambaut on 2011-04-20 10:13:02