Trouble setting up replication

I have been trying to set up "hot standby" replication, but have run
into problems, and hope someone here can help.

I have configured an ssh tunnel from a computer that is not on a public
IP, and was unable to figure out how to run pg_basebackup from that
server to backup the data from the main server, so I decided to run
pb_basebackup on the main server and copy it later. So I did this:

pg_basebackup -D /var/lib/pgsql/9.3/backups/rep/init -P -v -X s

(after a number of other attempts), and got errors. First I got a
permissions error, and found that the directory was owned by root
instead of postgres. I changed that, but eventually I got this error:

pg_basebackup: directory "/var/lib/pgsql/9.3/backups/rep" exists but is
not empty

So my question is whether I can safely delete the directory and run
pb_basebackup again?

I appreciate any help you can give. Let me know what additional
information is needed to answer the question.

Chuck