corrects bug when no format is specified

update results files

forgot about adding folder

update default options and correct bug

removes longest orf from aligned seq from results file

changed user.yml settings back to default

- forgot also to mention that when separating db by folder
 it can use multithreading

writes fasta files for aligned and db origin of longest orfs

download taxonomy only for working dir in scripts

each move has to be own command

maintains force_folder option prefix