Issue with Downloading Genomes from BVBRC

Question

[ryanmaroun3]

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.

[lifengyi]

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.

[GenoMax]

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.

Answer 1

[GenoMax]

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.