Question: Error on using BEAST
0
The Last Word • 170 wrote:
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.