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BEAUti 1.6.1 sequenceErrorModel xml not work in BEAST #436

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
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

Original issue reported on code.google.com by dong.w.xie@gmail.com on 1 Dec 2010 at 4:58

Attachments:

GoogleCodeExporter 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)

Original comment by dong.w.xie@gmail.com on 9 Dec 2010 at 10:06

GoogleCodeExporter commented 9 years ago

Original comment by dong.w.xie@gmail.com on 17 Feb 2011 at 9:31

GoogleCodeExporter 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.

Original comment by ramb...@gmail.com on 20 Apr 2011 at 7:45

GoogleCodeExporter 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).

Original comment by ramb...@gmail.com on 20 Apr 2011 at 10:13