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BEAST is giving an error on the xml file that I am using for an analysis. the full text of the error is
Random number seed: 1426841272890 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: 106.xml File encoding: Cp1252 Looking for plugins in C:\Documents and Settings\lib13\My Documents\Downloads\plugins Read alignment: alignment Sequences = 2 Sites = 1101 Datatype = nucleotide Site patterns 'patterns' created from positions 1-1101 of alignment 'alignment' unique pattern count = 23 Creating the tree model, 'treeModel' initial tree topology = (106.NK72R,106.O-1C244F) tree height = 1.280369814631102 Using strict molecular clock model. Creating state frequencies model 'frequencies': Initial frequencies = {0.25, 0.25, 0.25, 0.25} Creating HKY substitution model. Initial kappa = 2.0 Creating site model. Using BEAGLE TreeLikelihood Branch rate model used: strictClockBranchRates Using BEAGLE resource 0: CPU with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU Ignoring ambiguities in tree likelihood. With 23 unique site patterns. Using rescaling scheme : dynamic (rescaling every 100 evaluations) dr.xml.XMLParseException: Error parsing '<wideExchange>' element with id, 'null': Tree with fewer than 3 taxa 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.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) BEAST has terminated with an error. Please select QUIT from the menu. Mar 20, 2015 2:18:54 PM dr.app.beast.BeastMain <init> SEVERE: Parsing error - poorly formed BEAST file, 106.xml: Error parsing '<wideExchange>' element with id, 'null': Tree with fewer than 3 taxa java.lang.RuntimeException: Terminate at dr.app.beast.BeastMain.<init>(Unknown Source) at dr.app.beast.BeastMain.main(Unknown Source)
I have attached my file on dropbox and I am providing the link here. Please go through what error I am making and give suggestions.
The trees with fewer than 3 taxa error has been rectified by turning off the tree operators in the operators tab in BEAUTi since for two sequences, there is only one possible tree. However now I am stuck with
SEVERE: Parsing error - poorly formed BEAST file, 106.xml:
Error parsing '<uniformOperator>' element with id, 'null':
Hi, did you finally solve this problem, I'm stuck with the same thing, thanks for your answer.