While cloning, I had a similar issue [ my ERROR: Permission denied (publickey). fatal: Could not read from remote repository. Please make sure you have the correct access rights .. etc ]
-- I was using bitBucket/UBUNTU14.04 in my case, but ALREADY had a set of key files that I had previously generated AND I had changed the name of the files. I simply COPIED the files to the standard id_rsa & id_rsa.pub name format. I then re-ran the command with out issue.
OBTW: I could have also used the password prompt by using the HTTP style clone.