Generate new exception lists

1. Export the exception list:
   • gtdb -r power weighted_tree_exceptions --output --output output_file
2. Check manually the output file generated
3. Generate the 2 lists (Archaea and Bacteria):
   • exception_list_creation.py --exception_file EXCEPT_FILE --release_version RELEASE_ID
4. Get the Ids of the previous exception lists
   • gtdb genome_lists view --root
5. Set the previous exception lists to private:
   • gtdb genome_lists edit --list_id (id) --set_private

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How exception creation works:

There is 2 filters in the exception pipeline:

1. First Filter
   • Select genomes with Completeness >50 % and Contamination < 10% and Quality_Threshold > 50 % and with an NCBI taxonomy string.
   • For the selected genomes pick genomes where the order rank is not part of order ranks present in the set of genomes passing the normal filter (Completeness >60 & contamination < 10 & QT>60) or where the order is unknown