Program: 141245
Project: 141245
Buggy source:
/** 
 * Execute the analysis.
 * @throws EoulsanException if an error occurs while creating or executing theR script
 */
public void run() throws EoulsanException {
  final Map<String,Integer> conditionsMap=new HashMap<String,Integer>();
  final List<Integer> rSampleIds=new ArrayList<Integer>();
  final List<String> rSampleNames=new ArrayList<String>();
  final List<String> rCondNames=new ArrayList<String>();
  final List<Integer> rCondIndexes=new ArrayList<Integer>();
  final List<String> rCondRep=new ArrayList<String>();
  for (  Sample s : this.design.getSamples()) {
    if (!s.getMetadata().isConditionField())     throw new EoulsanException("String_Node_Str");
    if (!s.getMetadata().isReplicatTypeField())     throw new EoulsanException("String_Node_Str");
    final String condition=s.getMetadata().getCondition().trim();
    final String replicatType=s.getMetadata().getReplicatType().trim().toLowerCase();
    if ("String_Node_Str".equals(condition))     throw new EoulsanException("String_Node_Str" + s.getName() + "String_Node_Str"+ s.getId()+ "String_Node_Str");
    if (!("String_Node_Str".equals(replicatType) || "String_Node_Str".equals(replicatType)))     throw new EoulsanException("String_Node_Str" + replicatType + "String_Node_Str"+ s.getName()+ "String_Node_Str"+ s.getId()+ "String_Node_Str");
    if (!conditionsMap.containsKey(condition)) {
      conditionsMap.put(condition,conditionsMap.size() + 1);
      rCondNames.add(condition);
    }
    rSampleIds.add(s.getId());
    rSampleNames.add(s.getName());
    rCondIndexes.add(conditionsMap.get(condition));
    rCondRep.add(replicatType);
  }
  final StringBuilder sb=new StringBuilder();
  sb.append("String_Node_Str");
  sb.append(Globals.APP_NAME);
  sb.append("String_Node_Str");
  sb.append(Globals.APP_VERSION_STRING);
  sb.append("String_Node_Str");
  sb.append(new Date(System.currentTimeMillis()));
  sb.append("String_Node_Str");
  sb.append(readStaticScript());
  if (isBiologicalReplicates(rCondIndexes,rCondRep))   writeWithBiologicalReplicate(sb,rSampleIds,rSampleNames,rCondIndexes,rCondNames,rCondRep);
 else   writeWithoutBiologicalReplicate(sb,rSampleIds,rSampleNames,rCondIndexes,rCondNames);
  final File rScript;
  try {
    rScript=FileUtils.createTempFile(this.tempDir,"String_Node_Str","String_Node_Str");
    LOGGER.fine("String_Node_Str" + rScript.getAbsolutePath());
    Writer writer=FileUtils.createFastBufferedWriter(rScript);
    writer.write(sb.toString());
    writer.close();
    rScript.setExecutable(true);
  }
 catch (  IOException e) {
    throw new EoulsanException("String_Node_Str" + e.getMessage());
  }
  try {
    final ProcessBuilder pb=new ProcessBuilder("String_Node_Str","String_Node_Str",StringUtils.bashEscaping(rScript.getAbsolutePath()));
    pb.environment().put("String_Node_Str",this.tempDir.getAbsolutePath());
    ProcessUtils.logEndTime(pb.start(),pb.toString(),System.currentTimeMillis());
    if (!rScript.delete())     LOGGER.warning("String_Node_Str" + rScript.getAbsolutePath());
  }
 catch (  IOException e) {
    throw new EoulsanException("String_Node_Str" + e.getMessage());
  }
}

Fixed version (ground truth):
/** 
 * Execute the analysis.
 * @throws EoulsanException if an error occurs while creating or executing theR script
 */
public void run() throws EoulsanException {
  final Map<String,Integer> conditionsMap=new HashMap<String,Integer>();
  final List<Integer> rSampleIds=new ArrayList<Integer>();
  final List<String> rSampleNames=new ArrayList<String>();
  final List<String> rCondNames=new ArrayList<String>();
  final List<Integer> rCondIndexes=new ArrayList<Integer>();
  final List<String> rCondRep=new ArrayList<String>();
  for (  Sample s : this.design.getSamples()) {
    if (!s.getMetadata().isConditionField())     throw new EoulsanException("String_Node_Str");
    if (!s.getMetadata().isReplicatTypeField())     throw new EoulsanException("String_Node_Str");
    final String condition=s.getMetadata().getCondition().trim();
    final String replicatType=s.getMetadata().getReplicatType().trim().toLowerCase();
    if ("String_Node_Str".equals(condition))     throw new EoulsanException("String_Node_Str" + s.getName() + "String_Node_Str"+ s.getId()+ "String_Node_Str");
    if (!("String_Node_Str".equals(replicatType) || "String_Node_Str".equals(replicatType)))     throw new EoulsanException("String_Node_Str" + replicatType + "String_Node_Str"+ s.getName()+ "String_Node_Str"+ s.getId()+ "String_Node_Str");
    if (!conditionsMap.containsKey(condition)) {
      conditionsMap.put(condition,conditionsMap.size() + 1);
      rCondNames.add(condition);
    }
    rSampleIds.add(s.getId());
    rSampleNames.add(s.getName());
    rCondIndexes.add(conditionsMap.get(condition));
    rCondRep.add(replicatType);
  }
  final StringBuilder sb=new StringBuilder();
  sb.append("String_Node_Str");
  sb.append(Globals.APP_NAME);
  sb.append("String_Node_Str");
  sb.append(Globals.APP_VERSION_STRING);
  sb.append("String_Node_Str");
  sb.append(new Date(System.currentTimeMillis()));
  sb.append("String_Node_Str");
  sb.append(readStaticScript());
  if (isBiologicalReplicates(rCondIndexes,rCondRep))   writeWithBiologicalReplicate(sb,rSampleIds,rSampleNames,rCondIndexes,rCondNames,rCondRep);
 else   writeWithoutBiologicalReplicate(sb,rSampleIds,rSampleNames,rCondIndexes,rCondNames);
  final File rScript;
  try {
    rScript=FileUtils.createTempFile(this.tempDir,"String_Node_Str","String_Node_Str");
    LOGGER.fine("String_Node_Str" + rScript.getAbsolutePath());
    Writer writer=FileUtils.createFastBufferedWriter(rScript);
    writer.write(sb.toString());
    writer.close();
    rScript.setExecutable(true);
  }
 catch (  IOException e) {
    throw new EoulsanException("String_Node_Str" + e.getMessage());
  }
  try {
    final ProcessBuilder pb=new ProcessBuilder("String_Node_Str","String_Node_Str",rScript.getAbsolutePath());
    pb.environment().put("String_Node_Str",this.tempDir.getAbsolutePath());
    ProcessUtils.logEndTime(pb.start(),Joiner.on(' ').join(pb.command()),System.currentTimeMillis());
    if (!rScript.delete())     LOGGER.warning("String_Node_Str" + rScript.getAbsolutePath());
  }
 catch (  IOException e) {
    throw new EoulsanException("String_Node_Str" + e.getMessage());
  }
}