java.lang.RuntimeException: value cannot be null for attribute Exon.scoreType

GitHub | terrymun | 5 months ago
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    GFF source: ScoreType is required to parse the file but not required in GFF3 specs

    GitHub | 5 months ago | terrymun
    java.lang.RuntimeException: value cannot be null for attribute Exon.scoreType

    Root Cause Analysis

    1. java.lang.RuntimeException

      value cannot be null for attribute Exon.scoreType

      at org.intermine.xml.full.Item.setAttribute()
    2. org.intermine.xml
      Item.setAttribute
      1. org.intermine.xml.full.Item.setAttribute(Item.java:353)
      1 frame
    3. org.intermine.bio
      GFF3ConverterTask.execute
      1. org.intermine.bio.dataconversion.GFF3Converter.process(GFF3Converter.java:360)
      2. org.intermine.bio.dataconversion.GFF3Converter.parse(GFF3Converter.java:230)
      3. org.intermine.bio.task.GFF3ConverterTask.execute(GFF3ConverterTask.java:241)
      3 frames
    4. Ant
      UnknownElement.execute
      1. org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
      1 frame
    5. Java RT
      Method.invoke
      1. sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
      2. sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
      3. java.lang.reflect.Method.invoke(Method.java:606)
      3 frames
    6. Ant
      Ant.execute
      1. org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
      2. org.apache.tools.ant.Task.perform(Task.java:348)
      3. org.apache.tools.ant.Target.execute(Target.java:435)
      4. org.apache.tools.ant.Target.performTasks(Target.java:456)
      5. org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
      6. org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
      7. org.apache.tools.ant.Project.executeTargets(Project.java:1248)
      8. org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:440)
      8 frames
    7. org.intermine.task
      Integrate.execute
      1. org.intermine.task.Integrate.performAction(Integrate.java:219)
      2. org.intermine.task.Integrate.performAction(Integrate.java:131)
      3. org.intermine.task.Integrate.execute(Integrate.java:123)
      3 frames
    8. Ant
      UnknownElement.execute
      1. org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
      1 frame
    9. Java RT
      Method.invoke
      1. sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
      2. sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
      3. java.lang.reflect.Method.invoke(Method.java:606)
      3 frames
    10. Ant
      Main.startAnt
      1. org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
      2. org.apache.tools.ant.Task.perform(Task.java:348)
      3. org.apache.tools.ant.Target.execute(Target.java:435)
      4. org.apache.tools.ant.Target.performTasks(Target.java:456)
      5. org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
      6. org.apache.tools.ant.Project.executeTarget(Project.java:1364)
      7. org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
      8. org.apache.tools.ant.Project.executeTargets(Project.java:1248)
      9. org.apache.tools.ant.Main.runBuild(Main.java:851)
      10. org.apache.tools.ant.Main.startAnt(Main.java:235)
      10 frames
    11. Apache Ant Launcher
      Launcher.main
      1. org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
      2. org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
      2 frames