Hi @amaria.gallego!
Great! I just wanted to make sure, since your comment above ("Still I am having the error") sounded like you expected it to work after including --verbose - I realized I didn't clarify what the --verbose flag was for, and wanted to make sure you knew - no offense was intended!
Strange - there should be a lot more to that error message - in the future I recommend that you carefully review all of the output before copying and pasting - and in general its usually better to send us too much information, rather than too little!
Ah yes, are you referring to this?
I'm not sure how you edited your file in order to fix it, but I suspect that it just postponed the actual issue. Have you specifically contacted the sequencing center and asked about that empty read? Your best bet is to solve the problem at the source - the raw sequencing data.
Good luck and keep us posted!