Can't download unclassified organisms #206
Description
Hello,
I'm using taxonkit (last version, 0.12.0) to extract all taxids associated to one general taxid (ex: Alteromonadales, taxonkit list --show-rank --show-name --indent "" -i 135622 > output.txt).
outputTaxonkit_Alteromonadales.txt
Then, with ncbi-genome-download (last version, 0.3.1), I download fna, faa and gff files for some of the extracted taxids.
My issue happens when I want to download unclassified organisms (2614992, unclassified Alteromonas) :
ncbi-genome-download --section genbank --format protein-fasta,gff,fasta --taxids 2614992 bacteria
-> ERROR: No downloads matched your filter. Please check your options.
In fact, I can download unclassified organisms but with the specific taxid of the strain, 2961948 (Alteromonas sp. LMIT006, which is unclassified) but if the strain has the taxid 2614992, it's impossible to download it.
It shouldn't be an issue because I can download, for example, all needed files of strains, from "Shewanella algae" (38313).
My question is : why ncbi-genome-download doesn't have a direct access to these unclassified strains ?
Another thing is : the taxonomic name can changes but the unclassified organisms don't have this update...
ex: Gramelle became Christiangramia (https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=2705471)
Do you know why ?
Boulinguiez Matthieu,
Bioinformatics engineer, AFMB.