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kblin / ncbi-genome-download

Scripts to download genomes from the NCBI FTP servers
Apache License 2.0
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No downloads matched error #219

Closed tasha99 closed 2 months ago

tasha99 commented 10 months ago

Hello, I'm trying to download the entire Pseudomonas syringae species group fasta files. Im using the taxonomy ID 136849 but it keeos saying that there are no downloads that match this filter. The exact code I'm using is this:

ncbi-genome-download --formats fasta --species-taxid 136849 bacteria

Any idea how to overcome this issue? TIA

kblin commented 9 months ago

If I read the NCBI taxonomy database correctly. 136849 is a species group, not a species, so that likely won't be exposed in the dataset ncbi-genome-download is reading to calculate which files to download, namely the assembly_summary.txt file. My suggestion would be to use the gimme_taxa.py script for the contrib directory to grab a list of descendant taxids that ncbi-genome-download then does know how to download.

kblin commented 2 months ago

Closing stale question