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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";

Enter the Rast Username
username
...
" --domain "domainname
" --genetic_code "geneticcode
"