Program: 59712
Project: 59712
Buggy source:
@Override protected void internalParseXml(Element element) throws IOException {
  Element librariesElement=XmlHelper.getDistinctElementByName(element,KEY_ELEM_LIBRARIES);
  NodeList libraries=librariesElement.getElementsByTagName(KEY_ELEM_LIBRARY);
  this.libs=new ArrayList<>();
  for (int i=0; i < libraries.getLength(); i++) {
    this.libs.add(new Library((Element)libraries.item(i)));
  }
  Element pipelineElement=XmlHelper.getDistinctElementByName(element,KEY_ELEM_PIPELINE);
  Element mecqElement=XmlHelper.getDistinctElementByName(pipelineElement,KEY_ELEM_MECQ);
  this.mecqArgs=mecqElement == null ? null : new MecqArgs(mecqElement,this.rampartJobFileSystem.getMeqcDir(),this.getJobPrefix() + "String_Node_Str",this.libs);
  Element kmerReadsElement=XmlHelper.getDistinctElementByName(pipelineElement,KEY_ELEM_KMER_READS);
  this.kmerCountReadsArgs=kmerReadsElement == null ? null : new KmerCountReadsArgs(kmerReadsElement,this.libs,this.mecqArgs == null ? null : this.mecqArgs.getEqcArgList(),this.getJobPrefix() + "String_Node_Str",this.rampartJobFileSystem.getMeqcDir(),this.rampartJobFileSystem.getReadsKmersDir(),this.getOrganism());
  Element massElement=XmlHelper.getDistinctElementByName(pipelineElement,KEY_ELEM_MASS);
  this.massArgs=massElement == null ? null : new MassArgs(massElement,this.rampartJobFileSystem.getMassDir(),this.rampartJobFileSystem.getMeqcDir(),this.getJobPrefix() + "String_Node_Str",this.libs,this.mecqArgs == null ? null : this.mecqArgs.getEqcArgList(),this.getOrganism());
  Element ampElement=XmlHelper.getDistinctElementByName(pipelineElement,KEY_ELEM_AMP);
  this.ampArgs=ampElement == null ? null : new AmpArgs(ampElement,this.rampartJobFileSystem.getAmpDir(),this.getJobPrefix() + "String_Node_Str",this.rampartJobFileSystem.getMassOutFile(),this.libs,this.mecqArgs == null ? null : this.mecqArgs.getEqcArgList(),this.getOrganism());
  Element finaliseElement=XmlHelper.getDistinctElementByName(pipelineElement,KEY_ELEM_FINALISE);
  this.finaliseArgs=finaliseElement == null ? null : new FinaliseArgs(finaliseElement,this.ampArgs.getFinalAssembly(),this.rampartJobFileSystem.getFinalDir(),this.getOrganism(),this.getInstitution());
}

Fixed version (ground truth):
@Override protected void internalParseXml(Element element) throws IOException {
  Element librariesElement=XmlHelper.getDistinctElementByName(element,KEY_ELEM_LIBRARIES);
  NodeList libraries=librariesElement.getElementsByTagName(KEY_ELEM_LIBRARY);
  this.libs=new ArrayList<>();
  for (int i=0; i < libraries.getLength(); i++) {
    this.libs.add(new Library((Element)libraries.item(i),this.getOutputDir().getAbsoluteFile()));
  }
  Element pipelineElement=XmlHelper.getDistinctElementByName(element,KEY_ELEM_PIPELINE);
  Element mecqElement=XmlHelper.getDistinctElementByName(pipelineElement,KEY_ELEM_MECQ);
  this.mecqArgs=mecqElement == null ? null : new MecqArgs(mecqElement,this.rampartJobFileSystem.getMeqcDir(),this.getJobPrefix() + "String_Node_Str",this.libs);
  Element kmerReadsElement=XmlHelper.getDistinctElementByName(pipelineElement,KEY_ELEM_KMER_READS);
  this.kmerCountReadsArgs=kmerReadsElement == null ? null : new KmerCountReadsArgs(kmerReadsElement,this.libs,this.mecqArgs == null ? new ArrayList<EcqArgs>() : this.mecqArgs.getEqcArgList(),this.getJobPrefix() + "String_Node_Str",this.rampartJobFileSystem.getMeqcDir(),this.rampartJobFileSystem.getReadsKmersDir(),this.getOrganism());
  Element massElement=XmlHelper.getDistinctElementByName(pipelineElement,KEY_ELEM_MASS);
  this.massArgs=massElement == null ? null : new MassArgs(massElement,this.rampartJobFileSystem.getMassDir(),this.rampartJobFileSystem.getMeqcDir(),this.getJobPrefix() + "String_Node_Str",this.libs,this.mecqArgs == null ? new ArrayList<EcqArgs>() : this.mecqArgs.getEqcArgList(),this.getOrganism());
  Element ampElement=XmlHelper.getDistinctElementByName(pipelineElement,KEY_ELEM_AMP);
  this.ampArgs=ampElement == null ? null : new AmpArgs(ampElement,this.rampartJobFileSystem.getAmpDir(),this.getJobPrefix() + "String_Node_Str",this.rampartJobFileSystem.getMassOutFile(),this.libs,this.mecqArgs == null ? new ArrayList<EcqArgs>() : this.mecqArgs.getEqcArgList(),this.getOrganism());
  File finalAssembly=this.ampArgs == null ? this.rampartJobFileSystem.getMassOutFile() : this.ampArgs.getFinalAssembly();
  Element finaliseElement=XmlHelper.getDistinctElementByName(pipelineElement,KEY_ELEM_FINALISE);
  this.finaliseArgs=finaliseElement == null ? null : new FinaliseArgs(finaliseElement,finalAssembly,this.rampartJobFileSystem.getFinalDir(),this.getOrganism(),this.getInstitution());
}