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All genomes, regardless of where they were downloaded from, should be passed to the pipeline using the --ena_genomes flag. If any of your genomes were fetched using the fetch_ncbi.py script, you need to run CheckM on them and combine all completeness and contamination results into one file for all ENA and NCBI genomes. Pass the path to this combined file to the pipeline using the --ena_genomes_checkm flag.
We will adjust this in the future releases to avoid confusion.
Are we suppose to compile this data ourselves? fetch_ena.py seems to generate this data, but fetch_ncbi.py does not.
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