br302005

Thank you for such a quick response! Here is the output after I did `ls -l` :  Also, thank you for the suggestion about the fungal-specific repeats. I'm not...

I will add that after I ran this code there now is a Fungal library: `/RepeatMasker/Libraries/CONS-Dfam_3.1/Fungi` that contains 9 fungal-specific repeats.

That worked and the file can now run! How would you suggest fixing the library problem? Making a custom library of fungal repeats and running `-lib`? I see that RepBase...