Question: (Closed) Why can't I download bacterial genomes with wget?
0
gravatar for frenchmytoast112
3.4 years ago by
frenchmytoast11210 wrote:

Hello everyone,

is there a reason why I cannot download all the bacterial genomes with this command line with wget?

wget -r ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/*

 

I only get empty folders with nothing inside of each assembly.

Thanks!

 


 

genome • 1.2k views
ADD COMMENTlink written 3.4 years ago by frenchmytoast11210
1

Hello frenchmytoast112!

We believe that this post does not fit the main topic of this site.

Not a bioinformatics question. Also, try -m instead of -r

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink written 3.4 years ago by Devon Ryan90k

I cannot disagree more. Should this same question be closed and have been allowed in the first place?

Download All The Bacterial Genomes From Ncbi

ADD REPLYlink written 3.4 years ago by frenchmytoast11210

That question was specific to NCBI, this is a general "how do I use wget" question.

ADD REPLYlink written 3.4 years ago by Devon Ryan90k

Do you see the link to NCBI? Do you see that I mentioned bacterial genomes?  You are wrong. Its not a general wget question.

ADD REPLYlink written 3.4 years ago by frenchmytoast11210

Yes, I see both and that doesn't change my conclusion. If your question were:

"I'm trying to download all of the NCBI bacterial datasets but this command only seems to return XXX datasets when YYY are listed as being present on the webpage. Does anyone know where NCBI stores the remaining YYY-XXX datasets or is there something in the YYY number that I'm missing?"

then it'd be on topic.

ADD REPLYlink written 3.4 years ago by Devon Ryan90k

I see your conclusion, but do not agree with you premises. I would like to suggest to add a more welcoming tone your approach to post "that do not fit the main topic of the site". You seem of as an closed off community. But as a part of the bargain, next time I post I will explain the issue at hand with high detail and reproducible examples. This time you win, since I have already found the solution to my issue.

ADD REPLYlink written 3.4 years ago by frenchmytoast11210
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