Details
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Bug
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Status: Closed
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Blocker
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Resolution: Fixed
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None
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None
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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 -------------------------------