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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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doanload failed when groups is set to all #175

Closed showteeth closed 2 years ago

showteeth commented 3 years ago

When I download genome with: ncbi-genome-download --species-taxids 562 all, I got nothing. When I download genome with: ncbi-genome-download --species-taxids 562 bacteria, I got what I wanted. I wonder why there is such a difference? In my understanding, these two commands should get the same result.

kblin commented 3 years ago

Ah, that was a fun one to find. The issue is that RefSeq doesn't have a metagenome database, and we have logic to error out when you explicitly ask for ncbi-genome-download metagenomes (as a contrast ncbi-genome-download --section genbank metagenomes works), but the all logic didn't take that into account.

kblin commented 3 years ago

I'll release a new version of ncbi-genome-download with a fix on Monday, I don't have easy access to my release signing key right now.

showteeth commented 3 years ago

Thank you for your timely reply and look forward to new version!

showteeth commented 2 years ago

Sorry to interrupt, but did you forget to release a new version of ncbi-genome-download?

kblin commented 2 years ago

Yeah, I got distracted. But 0.3.1 is released now and should be on pypi already.