problems to run Beast

[Yamila Paula Cardoso]

Hi, when a run my file, I have this messages:

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.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.

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

line = dr.evomodel.treelikelihood.RootDiscreteStateStatistic

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

line = dr.evomodel.epidemiology.casetocase.operators.InfectionBranchGibbsOperator

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

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

Parsing XML file: alineadoBio.xml

  File encoding: MacRoman

Looking for plugins in /Users/yamilacardoso/Documents/plugins

Fatal error: 

Line number: 7245

Column number: 1

Error message: XML document structures must start and end within the same entity.

Sep 25, 2016 6:43:14 PM dr.app.beast.BeastMain <init>

SEVERE: Error running file: alineadoBio.xml

Sep 25, 2016 6:43:14 PM dr.app.beast.BeastMain <init>

SEVERE: Parsing error - poorly formed XML (possibly not an XML file):

XML document structures must start and end within the same entity.

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.

Where is the problem? my xml. file is attached

[Andrew Rambaut]

Dear Yamila,

The important error is this:

Fatal error: 
Line number: 7245
Column number: 1
Error message: XML document structures must start and end within the same entity.

If you look at your XML file you will see that it is corrupt (it ends prematurely and then has a repeated line). You will need to regenerate it.

Andrew

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<alineadoBio.xml.zip>

[JP]

I have recently gotten the same error. When I regenerate my file it still does not close. 

Is there a way to avoid this in the generation from BEAUTi. I know I could type all the parameters into the .xml file by hand, but that seems to defeat the purpose of BEAUTi.

Thanks!

-John