If you had printed the system command that you were running you would have figured this out.
Update
Just to show what I meant consider what happens when your code is modified like so:
my $command = qq("svr_submit_RAST_job --user "$username" --passwd "$Pa
+ssword" --fasta "$fasta" --domain "$domain" --genetic_code "$Genetic_
+code") ;
print "\n\n\nGoing to run the following through system:\n $command\n";
Output
Enter the Rast Username
username
Enter the Rast Password
password
Enter the fasta file Name
filename
Enter the Domain Name
domainname
Enter Genetic_Code
geneticcode
Going to run the following through system:
"svr_submit_RAST_job --user "username
" --passwd "password
" --fasta "filename
" --domain "domainname
" --genetic_code "geneticcode
"
And the newlines are there for you to see, as plain as daylight.