Issue with Downloading Genomes from BVBRC
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0
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3 months ago

Hey everyone!

I'm having problems with downloading genomes from the PATRIC database. I've been following this page: https://www.bv-brc.org/docs/quick_references/ftp.html I tried running the wget command on a text file with over 3,000 accession numbers, and nothing was downloaded.

This is the script I usually use:

mkdir -p Genomes
for i in `cat $1`; do 
    wget -qN "ftp://ftp.bvbrc.org/genomes/$i/$i.fna" 
    mv *.fna Genomes
done

I should also mention that this used to work well a couple of months ago, and I never had any issues with it up until now. Does anyone know what might have changed with the bvbrc database? How would I download genomes now?

Thank you in advance for any and all assistance.

BVBRC genomes • 460 views
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I'm using the BV-BRC ftp site for the first time, and run into the same issue.

So, I checked the ftp site with curl command and found that directory genomes/ no longer exist.

Below here are the directories the ftp site sitll contain :

"""

drwxrwxr-x 12 p3 p3 4096 Apr 9 2018 BRC_Mirrors

drwxrwxr-x 2 p3 p3 4096 Jan 3 2023 datasets

drwxr-xr-x 12 p3 p3 4096 Apr 8 2020 host_genomes

drwxr-xr-x 3 p3 p3 4096 Mar 16 2018 linkouts

drwxrwxr-x 4 p3 p3 4096 Sep 13 20:11 outbreaks

drwxr-xr-x 19 p3 p3 4096 Mar 10 2018 phyre2

-rw-rw-r-- 1 p3 p3 3799 Sep 13 00:44 README.txt

drwxr-xr-x 5 p3 p3 4096 Jun 15 17:53 RELEASE_NOTES

-rw-r--r-- 1 p3 p3 26 Aug 25 2021 robots.txt

drwxr-xr-x 4 p3 p3 4096 Jan 26 2018 software

drwxr-xr-x 4 p3 p3 4096 Jan 26 2018 specialty_genes

drwxrwxr-x 2 p3 p3 4096 May 3 2022 tmp

drwxrwxr-x 3 p3 p3 4096 Jul 9 20:26 transcriptomics

drwxr-xr-x 2 p3 p3 12288 Sep 13 00:29 viruses

drwxr-xr-x 9 p3 p3 4096 Jan 26 2018 workshops

"""

But I didn't find any notification for this change from the BV-BRC group, and the "ftp site" part of official docs of BV-BRC is not changed yet.

They don't provide an alternative option. The genomes/ directory just disappered secretly.

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Entering edit mode

You will have to email the group that manages the site to see what is going on. Sometimes website refreshes go wrong and perhaps that directory got omitted.

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Entering edit mode
3 months ago
GenoMax 147k

Since browsers no longer support ftp protocol, most places have made their ftp sites available via http/https connections. It looks like this site does not do that.

You could try adding --user=anonymous --password=your_email_address to the wget command above since logging in this way works via a FTP client.

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