difficulty running microsatellite analysis
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Norm
May 29, 2012, 4:40:47 PM5/29/12
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Hi,
I have been encountering crashes while attempting to run a 14 locus, 280 individual dataset. Basically, after the taxa are read, and the tree models are created, the output reads as follows:
...
tree height = 8.5930192959888
Using strict molecular clock model.
Using strict molecular clock model.
Using strict molecular clock model.
Using strict molecular clock model.
Using strict molecular clock model.
Using strict molecular clock model.
Using strict molecular clock model.
Using strict molecular clock model.
Using strict molecular clock model.
Using strict molecular clock model.
Using strict molecular clock model.
Using strict molecular clock model.
Using strict molecular clock model.
Using strict molecular clock model.
Error running file: MS.xml
Fatal exception: 78
java.lang.ArrayIndexOutOfBoundsException: 78
at dr.math.matrixAlgebra.RobustEigenDecomposition.tql2(Unknown Source)
at dr.math.matrixAlgebra.RobustEigenDecomposition.<init>(Unknown Source)
at dr.evomodel.substmodel.ComplexSubstitutionModel.setupMatrix(Unknown Source)
at dr.evomodel.substmodel.MicrosatelliteModel.setupMatrix(Unknown Source)
at dr.evomodel.substmodel.MicrosatelliteModel.computeTwoPhaseStationaryDistribution(Unknown Source)
at dr.evomodel.substmodel.TwoPhaseModel.computeStationaryDistribution(Unknown Source)
at dr.evomodel.substmodel.TwoPhaseModel.<init>(Unknown Source)
at dr.evomodelxml.substmodel.TwoPhaseModelParser.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)
Eddy:bin Norm$
...
78 is the maximum repeat length among any of the 14 loci (also the max of the first locus in the dataset). Providing each locus to its respective maximum under "sites" in BEAUti produces the same crash. Adding nonsense numbers also produces the same crash, except the message becomes
Fatal exception: [nonsense number]
java.lang.ArrayIndexOutOfBoundsException: [nonsense number]
What's going on?
I have been encountering crashes while attempting to run a 14 locus, 280 individual dataset. Basically, after the taxa are read, and the tree models are created, the output reads as follows:
...
tree height = 8.5930192959888
Using strict molecular clock model.
Using strict molecular clock model.
Using strict molecular clock model.
Using strict molecular clock model.
Using strict molecular clock model.
Using strict molecular clock model.
Using strict molecular clock model.
Using strict molecular clock model.
Using strict molecular clock model.
Using strict molecular clock model.
Using strict molecular clock model.
Using strict molecular clock model.
Using strict molecular clock model.
Using strict molecular clock model.
Error running file: MS.xml
Fatal exception: 78
java.lang.ArrayIndexOutOfBoundsException: 78
at dr.math.matrixAlgebra.RobustEigenDecomposition.tql2(Unknown Source)
at dr.math.matrixAlgebra.RobustEigenDecomposition.<init>(Unknown Source)
at dr.evomodel.substmodel.ComplexSubstitutionModel.setupMatrix(Unknown Source)
at dr.evomodel.substmodel.MicrosatelliteModel.setupMatrix(Unknown Source)
at dr.evomodel.substmodel.MicrosatelliteModel.computeTwoPhaseStationaryDistribution(Unknown Source)
at dr.evomodel.substmodel.TwoPhaseModel.computeStationaryDistribution(Unknown Source)
at dr.evomodel.substmodel.TwoPhaseModel.<init>(Unknown Source)
at dr.evomodelxml.substmodel.TwoPhaseModelParser.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)
Eddy:bin Norm$
...
78 is the maximum repeat length among any of the 14 loci (also the max of the first locus in the dataset). Providing each locus to its respective maximum under "sites" in BEAUti produces the same crash. Adding nonsense numbers also produces the same crash, except the message becomes
Fatal exception: [nonsense number]
java.lang.ArrayIndexOutOfBoundsException: [nonsense number]
What's going on?
bluejay
Aug 5, 2015, 9:11:11 AM8/5/15
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