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katylettuce / beast-mcmc

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Error generating a tree compatible with constraints #53

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. Run the attached XML

What do you see instead?

Parsing XML file: pp.rag.beast2.xml
Read alignment, 'alignment':
 Sequences = 9
     Sites = 4753
  Datatype = nucleotide
Site patterns 'patterns' created from positions 1-4753 of alignment 'alignment'
 pattern count = 221
Jun 4, 2008 3:30:23 PM dr.app.beast.BeastMain <init>
SEVERE: Error running file: pp.rag.beast2.xml
Jun 4, 2008 3:30:23 PM dr.app.beast.BeastMain <init>
SEVERE: Fatal exception (email the authors)
Fatal exception (email the authors)
java.lang.NullPointerException
    at dr.evolution.tree.SimpleTree.getNodeHeight(Unknown Source)
    at dr.evomodel.coalescent.CoalescentSimulator.attemptToScaleTree(Unknown Source)
    at dr.evomodel.coalescent.CoalescentSimulator.access$200(Unknown Source)
    at dr.evomodel.coalescent.CoalescentSimulator$1.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)

Original issue reported on code.google.com by ramb...@gmail.com on 4 Jun 2008 at 10:11

Attachments:

GoogleCodeExporter commented 9 years ago

Original comment by jhe...@gmail.com on 5 Jun 2008 at 12:19