Program: 11938
Project: 11938
Buggy source:
public static void main(String[] args) throws Exception {
  if (args.length != 2) {
    usage();
  }
  File input=new File(args[0]);
  if (!input.exists())   error("String_Node_Str" + input.getAbsolutePath() + "String_Node_Str");
  if (!input.canRead())   error("String_Node_Str" + input.getAbsolutePath());
  if (!input.isFile())   error("String_Node_Str" + input.getAbsolutePath());
  File output=new File(args[1]);
  if (output.exists())   error("String_Node_Str" + output.getAbsolutePath() + "String_Node_Str");
  if (output.canWrite())   error("String_Node_Str" + output.getAbsolutePath());
  if (output.isDirectory())   error("String_Node_Str" + output.getAbsolutePath());
  if (!output.getName().endsWith("String_Node_Str"))   error("String_Node_Str");
  BufferedReader in=new BufferedReader(new InputStreamReader(new BZip2CompressorInputStream(new FileInputStream(input))));
  BufferedOutputStream out=new BufferedOutputStream(new GZIPOutputStream(new FileOutputStream(output)));
  String line;
  int count=0;
  ProgressLogger progressLogger=new ProgressLogger(log,"String_Node_Str",100000,1000000);
  progressLogger.start();
  while ((line=in.readLine()) != null) {
    count++;
    progressLogger.tick();
    String[] tokens=line.split("String_Node_Str");
    if (tokens.length > 0) {
      if ((tokens.length == 3) && (tokens[0].trim().length() > 0) && (tokens[1].trim().length() > 0)&& (tokens[2].trim().length() > 0)) {
        output_resource(out,tokens[0],tokens[1],tokens[2]);
      }
 else       if ((tokens.length == 4) && (tokens[0].trim().length() > 0) && (tokens[1].trim().length() > 0)&& (tokens[3].trim().length() > 0)) {
        if (tokens[2].trim().length() == 0) {
          output_literal(out,tokens[0],tokens[1],tokens[3]);
        }
 else {
          if (tokens[2].startsWith(LANG)) {
            output_literal_lang(out,tokens[0],tokens[1],tokens[3],tokens[2]);
          }
 else {
            if (tokens[1].equals(OBJECT_KEY)) {
              output_literal2(out,tokens[0],tokens[1],tokens[2],tokens[3]);
            }
 else             if ((tokens[1].equals(OBJECT_NAME)) && (tokens[2].startsWith(GUID))) {
              output_literal2(out,tokens[0],tokens[1],tokens[2],tokens[3]);
            }
 else {
              log.warn("String_Node_Str",count,line);
            }
          }
        }
      }
 else {
        if (tokens.length < 3) {
          log.warn("String_Node_Str",new Object[]{count,tokens.length,line});
        }
 else {
          log.warn("String_Node_Str",new Object[]{count,line});
        }
      }
    }
  }
  progressLogger.finish();
}

Fixed version (ground truth):
public static void main(String[] args) throws Exception {
  if (args.length != 2) {
    usage();
  }
  File input=new File(args[0]);
  if (!input.exists())   error("String_Node_Str" + input.getAbsolutePath() + "String_Node_Str");
  if (!input.canRead())   error("String_Node_Str" + input.getAbsolutePath());
  if (!input.isFile())   error("String_Node_Str" + input.getAbsolutePath());
  File output=new File(args[1]);
  if (output.exists())   error("String_Node_Str" + output.getAbsolutePath() + "String_Node_Str");
  if (output.canWrite())   error("String_Node_Str" + output.getAbsolutePath());
  if (output.isDirectory())   error("String_Node_Str" + output.getAbsolutePath());
  if (!output.getName().endsWith("String_Node_Str"))   error("String_Node_Str");
  BufferedReader in=new BufferedReader(new InputStreamReader(new BZip2CompressorInputStream(new FileInputStream(input))));
  BufferedOutputStream out=new BufferedOutputStream(new GZIPOutputStream(new FileOutputStream(output)));
  String line;
  int count=0;
  ProgressLogger progressLogger=new ProgressLogger(log,"String_Node_Str",100000,1000000);
  progressLogger.start();
  while ((line=in.readLine()) != null) {
    count++;
    progressLogger.tick();
    String[] tokens=line.split("String_Node_Str");
    if (tokens.length > 0) {
      if ((tokens.length == 3) && (tokens[0].trim().length() > 0) && (tokens[1].trim().length() > 0)&& (tokens[2].trim().length() > 0)) {
        output_resource(out,tokens[0],tokens[1],tokens[2]);
      }
 else       if ((tokens.length == 4) && (tokens[0].trim().length() > 0) && (tokens[1].trim().length() > 0)&& (tokens[3].trim().length() > 0)) {
        if (tokens[2].trim().length() == 0) {
          output_literal(out,tokens[0],tokens[1],tokens[3]);
        }
 else {
          if (tokens[2].startsWith(LANG)) {
            output_literal_lang(out,tokens[0],tokens[1],tokens[3],tokens[2].substring(tokens[2].lastIndexOf('/') + 1));
          }
 else {
            if (tokens[1].equals(OBJECT_KEY)) {
              output_literal2(out,tokens[0],tokens[1],tokens[2],tokens[3]);
            }
 else             if ((tokens[1].equals(OBJECT_NAME)) && (tokens[2].startsWith(GUID))) {
              output_literal2(out,tokens[0],tokens[1],tokens[2],tokens[3]);
            }
 else {
              log.warn("String_Node_Str",count,line);
            }
          }
        }
      }
 else {
        if (tokens.length < 3) {
          log.warn("String_Node_Str",new Object[]{count,tokens.length,line});
        }
 else {
          log.warn("String_Node_Str",new Object[]{count,line});
        }
      }
    }
  }
  progressLogger.finish();
  out.flush();
  out.close();
}