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doanload failed when groups is set to all #175

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showteeth opened this issue Nov 20, 2021 · 5 comments
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doanload failed when groups is set to all #175

showteeth opened this issue Nov 20, 2021 · 5 comments
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@showteeth
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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.
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kblin commented Nov 20, 2021

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 added a commit that referenced this issue Nov 20, 2021
@kblin
core: Don't attempt to download metagenome info from refseq even if g…
306de29 
…roup is all

This should close issue #175

Signed-off-by: Kai Blin <kblin@biosustain.dtu.dk>
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kblin commented Nov 20, 2021

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.

@kblin kblin self-assigned this Nov 20, 2021
@showteeth
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Thank you for your timely reply and look forward to new version!

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

@showteeth showteeth reopened this Nov 30, 2021
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kblin commented Dec 1, 2021

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

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