Ganon Bct and Archaea whole genome DB seems to download fewer files than it should from NCBI

pirovc / ganon

ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hierarchical classification, customized reporting and more

https://pirovc.github.io/ganon/

MIT License

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Ganon Bct and Archaea whole genome DB seems to download fewer files than it should from NCBI #228

Closed shrivaa closed 1 year ago

shrivaa commented 1 year ago

Hi,

I was trying to create a local ganon DB. So, I downloaded the latest assembly, whole genome (top 1), bct and archea database files using ganon, this morning. I got 11,355 files from refseq.

However, there seem to be over 31K reseq files for these in NCBI, in the genbank DB. Any thoughts on what I am missing?

Thank you.

pirovc commented 1 year ago

Do you want genomes from refseq only or also genbank? Make sure the --source argument is properly set for ganon build. Could you share the command used?