Why can't I download bacterial genomes with wget?
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!
• 2,167 views
•
link
updated
by
Ram
•
written
by
frenchmytoast112 •
•
written
by
frenchmytoast112 •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
How to download protozoa reference genomes from NCBI
written by anna •
-
Having issues downloading reference bacteria genome from NCBI FTP website
written by krastegar0 •
-
Downloading only protein database sequences of bacteria and protozoa
written by Obex33 •
-
Uncommon wget behavior with ncbi genomes
written by flogin
-
download refseq of thousand of assembly file from NCBI
written by Shelle •
-
Download Assembly Files from NCBI Genomes Site in Batch
written by taraeicher •
-
Retrieve genbank viral genomes
written by erwan.scaon
-
Downloading microbial genomes
written by Bioaln
-
From accesion number to assemblies *.faa and *.pff
written by frenchmytoast112 •
-
Download All The Bacterial Genomes From Ncbi
written by rehma.ar •
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!
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
That question was specific to NCBI, this is a general "how do I use wget" question.
Do you see the link to NCBI? Do you see that I mentioned bacterial genomes? You are wrong. Its not a general wget question.
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.
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.