Program: 9739
Project: 9739
Buggy source:
private static void processQueryMode(LearningProblem lp,ReasonerComponent rs){
  logger.info("String_Node_Str" + "String_Node_Str" + "String_Node_Str");
  String queryStr="String_Node_Str";
  do {
    logger.info("String_Node_Str");
    BufferedReader input=new BufferedReader(new InputStreamReader(System.in));
    try {
      queryStr=input.readLine();
      logger.debug(queryStr);
    }
 catch (    IOException e) {
      e.printStackTrace();
    }
    if (!(queryStr.equalsIgnoreCase("String_Node_Str") || queryStr.equalsIgnoreCase("String_Node_Str"))) {
      Description concept=null;
      boolean parsedCorrectly=true;
      try {
        concept=KBParser.parseConcept(queryStr);
      }
 catch (      ParseException e1) {
        e1.printStackTrace();
        System.err.println("String_Node_Str");
        parsedCorrectly=false;
      }
catch (      TokenMgrError e) {
        e.printStackTrace();
        System.err.println("String_Node_Str");
        parsedCorrectly=false;
      }
      if (parsedCorrectly) {
        SortedSet<NamedClass> occurringConcepts=new TreeSet<NamedClass>(new ConceptComparator());
        occurringConcepts.addAll(Helper.getAtomicConcepts(concept));
        SortedSet<ObjectProperty> occurringRoles=new TreeSet<ObjectProperty>(new RoleComparator());
        occurringRoles.addAll(Helper.getAtomicRoles(concept));
        for (        NamedClass ac : rs.getNamedClasses())         occurringConcepts.remove(ac);
        for (        ObjectProperty ar : rs.getObjectProperties())         occurringRoles.remove(ar);
        boolean nonExistingConstructs=false;
        if (occurringConcepts.size() != 0 || occurringRoles.size() != 0) {
          logger.debug("String_Node_Str");
          if (occurringConcepts.size() > 0)           logger.debug("String_Node_Str" + occurringConcepts);
          if (occurringRoles.size() > 0)           logger.debug("String_Node_Str" + occurringRoles);
          nonExistingConstructs=true;
        }
        if (!nonExistingConstructs) {
          if (!queryStr.startsWith("String_Node_Str") && (queryStr.contains("String_Node_Str") || queryStr.contains("String_Node_Str"))) {
            logger.info("String_Node_Str");
          }
          logger.info("String_Node_Str" + concept.toKBSyntaxString() + "String_Node_Str");
          Set<Individual> result=null;
          result=rs.getIndividuals(concept);
          logger.info("String_Node_Str" + result.size() + "String_Node_Str"+ result);
          ScorePosNeg score=(ScorePosNeg)lp.computeScore(concept);
          logger.info(score);
        }
      }
    }
  }
 while (!(queryStr.equalsIgnoreCase("String_Node_Str") || queryStr.equalsIgnoreCase("String_Node_Str")));
}

Fixed version (ground truth):
private static void processQueryMode(LearningProblem lp,ReasonerComponent rs){
  logger.info("String_Node_Str" + "String_Node_Str" + "String_Node_Str");
  String queryStr="String_Node_Str";
  do {
    logger.info("String_Node_Str");
    BufferedReader input=new BufferedReader(new InputStreamReader(System.in));
    try {
      queryStr=input.readLine();
      logger.debug(queryStr);
    }
 catch (    IOException e) {
      e.printStackTrace();
    }
    if (!(queryStr.equalsIgnoreCase("String_Node_Str") || queryStr.equalsIgnoreCase("String_Node_Str"))) {
      Description concept=null;
      boolean parsedCorrectly=true;
      try {
        concept=KBParser.parseConcept(queryStr);
      }
 catch (      TokenMgrError e) {
        e.printStackTrace();
        System.err.println("String_Node_Str");
        parsedCorrectly=false;
      }
catch (      org.dllearner.parser.ParseException e) {
        e.printStackTrace();
        System.err.println("String_Node_Str");
        parsedCorrectly=false;
      }
      if (parsedCorrectly) {
        SortedSet<NamedClass> occurringConcepts=new TreeSet<NamedClass>(new ConceptComparator());
        occurringConcepts.addAll(Helper.getAtomicConcepts(concept));
        SortedSet<ObjectProperty> occurringRoles=new TreeSet<ObjectProperty>(new RoleComparator());
        occurringRoles.addAll(Helper.getAtomicRoles(concept));
        for (        NamedClass ac : rs.getNamedClasses())         occurringConcepts.remove(ac);
        for (        ObjectProperty ar : rs.getObjectProperties())         occurringRoles.remove(ar);
        boolean nonExistingConstructs=false;
        if (occurringConcepts.size() != 0 || occurringRoles.size() != 0) {
          logger.debug("String_Node_Str");
          if (occurringConcepts.size() > 0)           logger.debug("String_Node_Str" + occurringConcepts);
          if (occurringRoles.size() > 0)           logger.debug("String_Node_Str" + occurringRoles);
          nonExistingConstructs=true;
        }
        if (!nonExistingConstructs) {
          if (!queryStr.startsWith("String_Node_Str") && (queryStr.contains("String_Node_Str") || queryStr.contains("String_Node_Str"))) {
            logger.info("String_Node_Str");
          }
          logger.info("String_Node_Str" + concept.toKBSyntaxString() + "String_Node_Str");
          Set<Individual> result=null;
          result=rs.getIndividuals(concept);
          logger.info("String_Node_Str" + result.size() + "String_Node_Str"+ result);
          ScorePosNeg score=(ScorePosNeg)lp.computeScore(concept);
          logger.info(score);
        }
      }
    }
  }
 while (!(queryStr.equalsIgnoreCase("String_Node_Str") || queryStr.equalsIgnoreCase("String_Node_Str")));
}