Question: Error on using BEAST
0
gravatar for The Last Word
4.0 years ago by
The Last Word170
India
The Last Word170 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. 

beast • 2.8k views
ADD COMMENTlink modified 3.9 years ago • written 4.0 years ago by The Last Word170

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':

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by The Last Word170

Hi, did you finally solve this problem, I'm stuck with the same thing, thanks for your answer.

ADD REPLYlink written 3.0 years ago by javierahumada800
1
gravatar for The Last Word
3.9 years ago by
The Last Word170
India
The Last Word170 wrote:

If using only two sequences for BEAST analysis, please be sure to uncheck options specific to multiple sequences. If there are other technical errors, try installing and working on another PC. 

ADD COMMENTlink written 3.9 years ago by The Last Word170
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