Program: 59724
Project: 59724
Buggy source:
@Override public boolean execute(ExecutionContext executionContext) throws ProcessExecutionException, InterruptedException {
  try {
    log.info("String_Node_Str");
    MultiMassArgs args=(MultiMassArgs)this.getProcessArgs();
    List<File> unitigStatsFiles=new ArrayList<File>();
    List<File> contigStatsFiles=new ArrayList<File>();
    List<File> scaffoldStatsFiles=new ArrayList<File>();
    List<SingleMassArgs> singleMassArgsList=this.createSingleMassArgsList(args);
    List<Thread> singleMassThreads=new ArrayList<Thread>();
    Assembler assembler=AssemblerFactory.createAssembler(args.getAssembler());
    for (    SingleMassArgs singleMassArgs : singleMassArgsList) {
      if (assembler.makesUnitigs()) {
        unitigStatsFiles.add(new File(singleMassArgs.getUnitigsDir(),"String_Node_Str"));
      }
      if (assembler.makesContigs()) {
        contigStatsFiles.add(new File(singleMassArgs.getContigsDir(),"String_Node_Str"));
      }
      if (assembler.makesScaffolds()) {
        scaffoldStatsFiles.add(new File(singleMassArgs.getScaffoldsDir(),"String_Node_Str"));
      }
      if (!singleMassArgs.getOutputDir().exists() && !singleMassArgs.getOutputDir().mkdirs()) {
        throw new IOException("String_Node_Str");
      }
      this.singleMassExecutor.executeSingleMass(singleMassArgs,this.conanProcessService,executionContext);
    }
    if (args.getParallelismLevel().doParallelMass()) {
      log.debug("String_Node_Str");
      this.executeScheduledWait(args.getJobPrefix(),args.getOutputDir(),executionContext);
    }
    log.info("String_Node_Str");
    log.info("String_Node_Str");
    File statsDir=new File(args.getOutputDir(),"String_Node_Str");
    if (assembler.makesUnitigs()) {
      executeMassSelector(args,new File(statsDir,"String_Node_Str"),unitigStatsFiles,executionContext);
    }
    if (assembler.makesContigs()) {
      executeMassSelector(args,new File(statsDir,"String_Node_Str"),contigStatsFiles,executionContext);
    }
    if (assembler.makesScaffolds()) {
      executeMassSelector(args,new File(statsDir,"String_Node_Str"),scaffoldStatsFiles,executionContext);
    }
    log.info("String_Node_Str");
  }
 catch (  IOException ioe) {
    throw new ProcessExecutionException(-1,ioe);
  }
  return true;
}

Fixed version (ground truth):
@Override public boolean execute(ExecutionContext executionContext) throws ProcessExecutionException, InterruptedException {
  try {
    log.info("String_Node_Str");
    MultiMassArgs args=(MultiMassArgs)this.getProcessArgs();
    List<File> unitigStatsFiles=new ArrayList<File>();
    List<File> contigStatsFiles=new ArrayList<File>();
    List<File> scaffoldStatsFiles=new ArrayList<File>();
    List<SingleMassArgs> singleMassArgsList=this.createSingleMassArgsList(args);
    List<Thread> singleMassThreads=new ArrayList<Thread>();
    Assembler assembler=AssemblerFactory.createAssembler(args.getAssembler());
    assembler.getArgs().setLibraries(args.getLibs());
    for (    SingleMassArgs singleMassArgs : singleMassArgsList) {
      if (assembler.makesUnitigs()) {
        unitigStatsFiles.add(new File(singleMassArgs.getUnitigsDir(),"String_Node_Str"));
      }
      if (assembler.makesContigs()) {
        contigStatsFiles.add(new File(singleMassArgs.getContigsDir(),"String_Node_Str"));
      }
      if (assembler.makesScaffolds()) {
        scaffoldStatsFiles.add(new File(singleMassArgs.getScaffoldsDir(),"String_Node_Str"));
      }
      if (!singleMassArgs.getOutputDir().exists() && !singleMassArgs.getOutputDir().mkdirs()) {
        throw new IOException("String_Node_Str");
      }
      this.singleMassExecutor.executeSingleMass(singleMassArgs,this.conanProcessService,executionContext);
    }
    if (args.getParallelismLevel().doParallelMass()) {
      log.debug("String_Node_Str");
      this.executeScheduledWait(args.getJobPrefix(),args.getOutputDir(),executionContext);
    }
    log.info("String_Node_Str");
    log.info("String_Node_Str");
    File statsDir=new File(args.getOutputDir(),"String_Node_Str");
    if (assembler.makesUnitigs()) {
      executeMassSelector(args,new File(statsDir,"String_Node_Str"),unitigStatsFiles,executionContext);
    }
    if (assembler.makesContigs()) {
      executeMassSelector(args,new File(statsDir,"String_Node_Str"),contigStatsFiles,executionContext);
    }
    if (assembler.makesScaffolds()) {
      executeMassSelector(args,new File(statsDir,"String_Node_Str"),scaffoldStatsFiles,executionContext);
    }
    log.info("String_Node_Str");
  }
 catch (  IOException ioe) {
    throw new ProcessExecutionException(-1,ioe);
  }
  return true;
}