Same thing as my previous comment and given that you are just opening the files and not doing anything with them, you could probably merge this loop and the next one. Then instead of raising an error per file you could store all the filenames that failed in a list and then print out that list.

```python
broken_fps = []

for fp in qual_files + fast_files:
    try:
        # check the file can be opened
    except:
        broken_fps.append(fp)

if broken_fps:
    option_parser.error('There was a problem opening the following files %s' % ', '.join(broken_fps))
```