Using BufferedReader.readLine() in a while loop properly

In case if you are still stumbling over this question. Nowadays things look nicer with Java 8:

try {
  Files.lines(Paths.get(targetsFile)).forEach(
    s -> {
      System.out.println(s);
      // do more stuff with s
    }
  );
} catch (IOException exc) {
  exc.printStackTrace();
}

You can use a structure like the following:

 while ((line = bufferedReader.readLine()) != null) {
            System.out.println(line);
        }

You're calling br.readLine() a second time inside the loop.
Therefore, you end up reading two lines each time you go around.

also very comprehensive...

try{
    InputStream fis=new FileInputStream(targetsFile);
    BufferedReader br=new BufferedReader(new InputStreamReader(fis));

    for (String line = br.readLine(); line != null; line = br.readLine()) {
       System.out.println(line);
    }

    br.close();
}
catch(Exception e){
    System.err.println("Error: Target File Cannot Be Read");
}