# 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?