Please edit this to make it more concise, this is way to long and badly structured, don't just copy paste irrelevant stuff. Looks like you are trolling! What is your problem here, which commands use the source-code tag to clearly mark what command you call and what output you get. Pls, really edit this, otherwise I will mark it for deletion.

Oh yeah, and btw, get your head right about the unix shell. You are creating an empty directory and then wonder why ls shows it's empty. But maybe Im waisting my time here anyway, you don't seem to listen to the comments you get.

I think this should probably be closed. It's off topic, and a very bad question. I suggest coming back when you've learnt how Linux works, and trying to ask some Bioinformatics questions.