Thanks for that, it does output to a text file now, but it has "doubles" of every output and it's all in one file, as opposed to every output of 5000 sequences being in a separate file. I don't think there is any need to rewrite the perl script though, he was using this script and generating the separate files. I just don't know the correct way to execute it with the proper switches or formatting to make that happen. I don't think this guy (before me) wrote scripts, just used available ones.