Uploaded image for project: 'Barna Package'
  1. Barna Package
  2. BARNA-158

Error model fails to load with Java 1.7

    XMLWordPrintable

Details

    • Bug
    • Status: Closed
    • Blocker
    • Resolution: Fixed
    • None
    • None
    • Simulator
    • None

    Description

      There seems to be a problem with loading the simulator error models in java 1.7.

      Seems to be related to the XStream library.

      [INFO] Reading error model 76 bases model
      [ERROR] Unable to load error model : Cannot construct
      fbi.genome.sequencing.rnaseq.simulation.error.QualityTransitions as it
      does not have a no-args constructor
      ---- Debugging information ----
      message             : Cannot construct
      fbi.genome.sequencing.rnaseq.simulation.error.QualityTransitions as it
      does not have a no-args constructor
      cause-exception     :
      com.thoughtworks.xstream.converters.reflection.ObjectAccessException
      cause-message       : Cannot construct
      fbi.genome.sequencing.rnaseq.simulation.error.QualityTransitions as it
      does not have a no-args constructor
      class               :
      fbi.genome.sequencing.rnaseq.simulation.error.QualityErrorModel
      required-type       :
      fbi.genome.sequencing.rnaseq.simulation.error.QualityTransitions
      path                :
      /fbi.genome.sequencing.rnaseq.simulation.error.QualityErrorModel/qualityModel
      line number         : 2
      -------------------------------
      com.thoughtworks.xstream.converters.ConversionException: Cannot
      construct fbi.genome.sequencing.rnaseq.simulation.error.QualityTransitions
      as it does not have a no-args constructor
      ---- Debugging information ----
      message             : Cannot construct
      fbi.genome.sequencing.rnaseq.simulation.error.QualityTransitions as it
      does not have a no-args constructor
      cause-exception     :
      com.thoughtworks.xstream.converters.reflection.ObjectAccessException
      cause-message       : Cannot construct
      fbi.genome.sequencing.rnaseq.simulation.error.QualityTransitions as it
      does not have a no-args constructor
      class               :
      fbi.genome.sequencing.rnaseq.simulation.error.QualityErrorModel
      required-type       :
      fbi.genome.sequencing.rnaseq.simulation.error.QualityTransitions
      path                :
      /fbi.genome.sequencing.rnaseq.simulation.error.QualityErrorModel/qualityModel
      line number         : 2
      -------------------------------
      at com.thoughtworks.xstream.core.TreeUnmarshaller.convert(TreeUnmarshaller.java:63)
      at com.thoughtworks.xstream.core.AbstractReferenceUnmarshaller.convert(AbstractReferenceUnmarshaller.java:45)
      at com.thoughtworks.xstream.core.TreeUnmarshaller.convertAnother(TreeUnmarshaller.java:46)
      at com.thoughtworks.xstream.annotations.AnnotationReflectionConverter.unmarshallField(AnnotationReflectionConverter.java:66)
      at com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.doUnmarshal(AbstractReflectionConverter.java:188)
      at com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.unmarshal(AbstractReflectionConverter.java:125)
      at com.thoughtworks.xstream.core.TreeUnmarshaller.convert(TreeUnmarshaller.java:56)
      at com.thoughtworks.xstream.core.AbstractReferenceUnmarshaller.convert(AbstractReferenceUnmarshaller.java:45)
      at com.thoughtworks.xstream.core.TreeUnmarshaller.convertAnother(TreeUnmarshaller.java:46)
      at com.thoughtworks.xstream.core.TreeUnmarshaller.start(TreeUnmarshaller.java:117)
      at com.thoughtworks.xstream.core.ReferenceByXPathMarshallingStrategy.unmarshal(ReferenceByXPathMarshallingStrategy.java:29)
      at com.thoughtworks.xstream.XStream.unmarshal(XStream.java:846)
      at com.thoughtworks.xstream.XStream.unmarshal(XStream.java:833)
      at com.thoughtworks.xstream.XStream.fromXML(XStream.java:789)
      at fbi.genome.sequencing.rnaseq.simulation.error.MarkovErrorModel.loadErrorModel(MarkovErrorModel.java:325)
      at fbi.genome.sequencing.rnaseq.simulation.Sequencer.loadErrors(Sequencer.java:216)
      at fbi.genome.sequencing.rnaseq.simulation.SimulationPipeline.call(SimulationPipeline.java:306)
      at fbi.genome.sequencing.rnaseq.simulation.SimulationPipeline.call(SimulationPipeline.java:32)
      at fbi.commons.flux.Flux.main(Flux.java:182)
      Caused by: com.thoughtworks.xstream.converters.reflection.ObjectAccessException:
      Cannot construct
      fbi.genome.sequencing.rnaseq.simulation.error.QualityTransitions as it
      does not have a no-args constructor
      at com.thoughtworks.xstream.converters.reflection.PureJavaReflectionProvider.newInstance(PureJavaReflectionProvider.java:59)
      at com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.instantiateNewInstance(AbstractReflectionConverter.java:257)
      at com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.unmarshal(AbstractReflectionConverter.java:124)
      at com.thoughtworks.xstream.core.TreeUnmarshaller.convert(TreeUnmarshaller.java:56)
      ... 18 more
      [ERROR] Unable to load error model : Cannot construct
      fbi.genome.sequencing.rnaseq.simulation.error.QualityTransitions as it
      does not have a no-args constructor
      ---- Debugging information ----
      message             : Cannot construct
      fbi.genome.sequencing.rnaseq.simulation.error.QualityTransitions as it
      does not have a no-args constructor
      cause-exception     :
      com.thoughtworks.xstream.converters.reflection.ObjectAccessException
      cause-message       : Cannot construct
      fbi.genome.sequencing.rnaseq.simulation.error.QualityTransitions as it
      does not have a no-args constructor
      class               :
      fbi.genome.sequencing.rnaseq.simulation.error.QualityErrorModel
      required-type       :
      fbi.genome.sequencing.rnaseq.simulation.error.QualityTransitions
      path                :
      /fbi.genome.sequencing.rnaseq.simulation.error.QualityErrorModel/qualityModel
      line number         : 2
      -------------------------------
      

      Attachments

        Activity

          People

            thasso Thasso Griebel
            thasso Thasso Griebel
            Votes:
            0 Vote for this issue
            Watchers:
            2 Start watching this issue

            Dates

              Created:
              Updated:
              Resolved:

              Time Tracking

                Estimated:
                Original Estimate - 2 hours
                2h
                Remaining:
                Remaining Estimate - 2 hours
                2h
                Logged:
                Time Spent - Not Specified
                Not Specified