Why does RATT create a directory with chromosome sequences and how can I stop it? I have run RATT to transfer the annotation from a reference strain to another strain. For this, I have run:

$RATT_HOME/start.ratt.sh embl ref.fa output/annotation/ Strain


This creates several things in the working directory that I do not wish: 


a Sequences folder with the sequence in FASTA format of each chromosome
a copy of the reference sequence in FASTA format (followed by a mysterious number)
a copy of the query sequence in FASTA format followed by a mysterious number


I could not find any options in the RATT help to disable the creation of these files. Also, does anybody know why these files are created?
RATT seems to be a very simple wrapper script that unfortunately does not clean up its temporary files properly. Short of modifying the code yourself, your only option is to perform the cleanup manually after running RATT.

The temporary copies are made because (a) the query is not an exact copy: RATT performs some cleaning. And (b) it needs to extract a FASTA file from the EMBL input for use in downstream tools.

The “mysterious” number behind the file names is simply the process ID of the RATT process. This is appended to make these intermediate files more or less unique (presumably to prevent overwriting existing files).