Program: 59743
Project: 59743
Buggy source:
@Override public boolean execute(ExecutionContext executionContext) throws ProcessExecutionException, InterruptedException {
  try {
    QTArgs args=(QTArgs)this.getProcessArgs();
    if ((args.getTool() == null || args.getTool().isEmpty()) && (args.getConfig() != null && args.getConfig().exists())) {
      args=QTArgs.parseConfig(args.getConfig());
    }
    String qtType=args.getTool();
    List<Library> libs=args.getLibs();
    SchedulerArgs backupArgs=null;
    SchedulerArgs copyArgs=null;
    if (executionContext.usingScheduler()) {
      backupArgs=executionContext.getScheduler().getArgs();
      copyArgs=executionContext.getScheduler().getArgs().copy();
      copyArgs.setBackgroundTask(true);
      executionContext.getScheduler().setArgs(copyArgs);
    }
    List<QualityTrimmer> qtList=args.createQualityTrimmers(this);
    String jobPrefix=(copyArgs.getJobName() != null && !copyArgs.getJobName().trim().isEmpty()) ? backupArgs.getJobName().trim() : "String_Node_Str";
    int i=1;
    for (    QualityTrimmer qt : qtList) {
      if (executionContext.usingScheduler()) {
        String jobName=jobPrefix + "String_Node_Str" + qt.getName()+ "String_Node_Str"+ i++;
        log.debug("String_Node_Str" + jobName);
        executionContext.getScheduler().getArgs().setJobName(jobName);
        executionContext.getScheduler().getArgs().setMonitorFile(new File(((QTArgs)this.getProcessArgs()).getOutputDir(),jobName + "String_Node_Str"));
      }
      this.conanProcessService.execute(qt,executionContext);
    }
    if (executionContext.usingScheduler()) {
      this.conanProcessService.waitFor(executionContext.getScheduler().createWaitCondition(ExitStatus.Type.COMPLETED_SUCCESS,jobPrefix + "String_Node_Str"),executionContext);
    }
    createConfigs(qtList,args);
  }
 catch (  IOException ioe) {
    throw new ProcessExecutionException(-1,ioe);
  }
  return true;
}

Fixed version (ground truth):
@Override public boolean execute(ExecutionContext executionContext) throws ProcessExecutionException, InterruptedException {
  try {
    QTArgs args=(QTArgs)this.getProcessArgs();
    if ((args.getTool() == null || args.getTool().isEmpty()) && (args.getConfig() != null && args.getConfig().exists())) {
      QTArgs configArgs=QTArgs.parseConfig(args.getConfig());
      args.setMinLen(configArgs.getMinLen());
      args.setMinQual(configArgs.getMinQual());
      args.setTool(configArgs.getTool());
      args.setLibs(configArgs.getLibs());
    }
    String qtType=args.getTool();
    List<Library> libs=args.getLibs();
    SchedulerArgs backupArgs=null;
    SchedulerArgs copyArgs=null;
    String jobPrefix="String_Node_Str";
    if (executionContext.usingScheduler()) {
      backupArgs=executionContext.getScheduler().getArgs();
      copyArgs=executionContext.getScheduler().getArgs().copy();
      copyArgs.setBackgroundTask(true);
      executionContext.getScheduler().setArgs(copyArgs);
      jobPrefix=(copyArgs.getJobName() != null && !copyArgs.getJobName().trim().isEmpty()) ? backupArgs.getJobName().trim() : "String_Node_Str";
    }
    List<QualityTrimmer> qtList=args.createQualityTrimmers(this);
    int i=1;
    for (    QualityTrimmer qt : qtList) {
      if (executionContext.usingScheduler()) {
        String jobName=jobPrefix + "String_Node_Str" + qt.getName()+ "String_Node_Str"+ i++;
        log.debug("String_Node_Str" + jobName);
        executionContext.getScheduler().getArgs().setJobName(jobName);
        executionContext.getScheduler().getArgs().setMonitorFile(new File(((QTArgs)this.getProcessArgs()).getOutputDir(),jobName + "String_Node_Str"));
      }
      this.conanProcessService.execute(qt,executionContext);
    }
    if (executionContext.usingScheduler()) {
      this.conanProcessService.waitFor(executionContext.getScheduler().createWaitCondition(ExitStatus.Type.COMPLETED_SUCCESS,jobPrefix + "String_Node_Str"),executionContext);
    }
    createConfigs(qtList,args);
  }
 catch (  IOException ioe) {
    throw new ProcessExecutionException(-1,ioe);
  }
  return true;
}