Open Ahmed-Shibl opened 1 year ago
Hi, maybe you figured this out. ncbi-genome-download creates a cache file, which contains the metadata you need. If you run:
ncbi-genome-download -h
it will then produce these lines in the helpfile:
-N, --no-cache Don't cache the assembly summary file in
/cluster/home/thhaverk/.cache/ncbi-genome-download.
So if you do a dry run, you will have the metadata file in the cache folder
First I want to thank you for this great tool!
I wanted to ask if there was an option to get the metadata file for a list of accessions without downloading the genomes. I would like to refine the number of genomes that I download based on their metadata.
I tried this command in an attempt to generate the
ALL_actino_accs_in_tree_metadata.txt
file:ncbi-genome-download --dry-run --section genbank --assembly-level all --assembly-accessions ALL_actino_accs_in_tree.txt --output-folder /Obesity_v2/actinobacteriota/anvio --metadata ALL_actino_accs_in_tree_metadata.txt --progress-bar --verbose bacteria
No file was generated but this was the output:
Please let me know if you would need any other information. Thanks!