Error message in BEAST 1.8.2 when I tried to run microsatellite data

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jlquei...@gmail.com

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Jul 19, 2015, 4:29:46 AM7/19/15
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Hey guys,

I think that the error message (below) was already reported by an user of BEAST. However, I did not find the solution for that. The question is that I'm trying to run a microsatellite database with 850 individuals and 35 loci, but the same error message comes out. 

Has anyone the way to solve the problem?

Thank you before hand for your help.

Cheers,

Joao 

Failed to load parser: dr.inferencexml.trace.GeneralizedHarmonicMeanAnalysisParser
line = dr.inferencexml.trace.GeneralizedHarmonicMeanAnalysisParser


Loading additional development parsers from development_parsers.properties, which is additional set of parsers only available for development version ...

WARNING: parser - dr.app.beagle.multidimensionalscaling.MultiDimensionalScalingLikelihood in development_parsers.properties is duplicated, which is REPLACING the same parser loaded previously.

Parsing XML file: Database_with_New_POP_IBERIA.micros3.xml
  File encoding: MacRoman
Looking for plugins in /Users/Joao/Desktop/POPULATIONGENETICS2/MICROS/BEAST/Constante_size_10E_4clock/plugins

BEAST has terminated with an error. Please select QUIT from the menu.
Fatal exception: 
2 can not be converted. State needs to be an integer or unknown (?).
java.lang.NumberFormatException: 
2 can not be converted. State needs to be an integer or unknown (?).
at dr.evolution.datatype.Microsatellite.getState(Unknown Source)
at dr.evoxml.MicrosatellitePatternParser.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)
java.lang.RuntimeException: Terminate
at dr.app.beast.BeastMain.<init>(Unknown Source)
at dr.app.beast.BeastMain.main(Unknown Source)

Mahwash Jamy

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Jan 18, 2016, 6:08:42 AM1/18/16
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Hi Joao,

I just came across this post and would be interested to hear if you managed to find a solution. I'm getting the same error message but have failed to find a solution online.

Cheers,
Mahwash

JenR

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Jan 20, 2016, 3:43:05 AM1/20/16
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I'm having same issue --> I'll let you know if I figure anything out. 

Good luck!
Jen

Andrew Rambaut

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Jan 20, 2016, 3:45:34 AM1/20/16
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Dear Jen & Mahwash,

You could try the pre-release of version 1.8.3 - I fixed a couple of issues with reading
microsat data:


If the issue is still there you could leave a description in the bug tracker:


Thanks,
Andrew

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Mahwash Jamy

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Jan 20, 2016, 9:51:50 AM1/20/16
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Thanks Andrew!!

Natalia Bayona

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Jul 7, 2016, 4:58:40 PM7/7/16
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Dear Andrew,

I am using version 1.8.3 and I have created the xml file for microsat data in order to analyze EBSP(I use the EBSP tutorial to create it). But when I am running Beast I am having the following error. I have been looking for similar error in this and other forums but I cannot find the solution.

I appreciate all the support.

Failed to load BEAGLE library: no hmsbeagle64 in java.library.path
Failed to load BEAGLE library: no hmsbeagle64 in java.library.path
BEAGLE not installed/found


Random number seed: 1467924064494


Failed to load parser: dr.inferencexml.trace.GeneralizedHarmonicMeanAnalysisParser
line = dr.inferencexml.trace.GeneralizedHarmonicMeanAnalysisParser



Failed to load parser: dr.evomodel.treelikelihood.RootDiscreteStateStatistic
line = dr.evomodel.treelikelihood.RootDiscreteStateStatistic


Loading additional development parsers from development_parsers.properties, which is additional set of parsers only available for development version ...

WARNING: parser - dr.inferencexml.model.DifferenceParameterParser in development_parsers.properties is duplicated, which is REPLACING the same parser loaded previously.

WARNING: parser - dr.inferencexml.model.SumParameterParser in development_parsers.properties is duplicated, which is REPLACING the same parser loaded previously.

WARNING: parser - dr.evomodelxml.operators.SubtreeJumpOperatorParser in development_parsers.properties is duplicated, which is REPLACING the same parser loaded previously.


Failed to load parser: dr.evomodel.epidemiology.casetocase.operators.InfectionBranchGibbsOperator
line = dr.evomodel.epidemiology.casetocase.operators.InfectionBranchGibbsOperator

WARNING: parser - dr.app.beagle.multidimensionalscaling.MultiDimensionalScalingLikelihood in development_parsers.properties is duplicated, which is REPLACING the same parser loaded previously.

Parsing XML file: East_Pac_beast.xml
  File encoding: Cp1252
Looking for plugins in C:\Users\Natalia\Google Drive\D\plugins
dr.xml.XMLParseException: Error parsing '<microsatellitePattern>' element with id, 'Chi008':
Unable to parse microsatellite data: 
144 can not be converted. State needs to be an integer or unknown (?).
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)
Jul 07, 2016 3:41:19 PM dr.app.beast.BeastMain <init>
SEVERE: Parsing error - poorly formed BEAST file, East_Pac_beast.xml:
Error parsing '<microsatellitePattern>' element with id, 'Chi008':
Unable to parse microsatellite data: 
144 can not be converted. State needs to be an integer or unknown (?).
java.lang.RuntimeException: Terminate
at dr.app.beast.BeastMain.<init>(Unknown Source)
at dr.app.beast.BeastMain.main(Unknown Source)

BEAST has terminated with an error. Please select QUIT from the menu.
PhD. Natalia Juliana Bayona Vásquez
Posdoctoral Researcher
Laboratorio de Genética de Organismos Acuáticos
Universidad Nacional Autónoma de México
Mexico City
Tel: 52-5529608256

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