@MiriamGorostidi,
I've broken this answer out into its own post, to prevent cluttering the more interesting questions you posted here.
This error message pops up when you enter a command without some required inputs. It sure looks like you entered them, so why is your terminal ignoring them? My guess is that there is an invisible whitespace character like " " or LF after the \ on the first line. Try again, making sure the \ is the last character on any line where you use it. More details here.
If this doesn't help you fix this problem, please put relevant responses on this new topic instead of on your broader bioinformatics question.
