[BUG] anvi-setup-ncbi-cogs urlopen error about anvio

[ivagljiva]

Hmm, this actually looks like the new FTP link (the old one used to start with ftp://ftp.ncbi.nih.gov, but the link in the error message has ftp://ftp.ncbi.nlm.nih.gov). Which makes sense because @meren patched the v8 release recently. So perhaps there is still an issue here, but it shouldn't be something that you need to configure yourself. I am looking into it.

[Ge0rges]

Hi @Lcornet NCBI recently changed the URL they use so the v8 of Anvio is out of date. If you install the development version (instructions here) this bug is fixed.

Edit: This is wrong.

[ivagljiva]

I started with a fresh install of anvi'o v8 and ran anvi-setup-ncbi-cogs --debug -T 4. It worked for me (and it used the new NCBI FTP link), so no issues with the codebase or installation instructions here.

@Lcornet, I wonder if there is some sort of issue blocking downloads from the terminal. Are you able to run curl ftp://ftp.ncbi.nlm.nih.gov/pub/COG/COG2020/data/cog-20.cog.csv -I? The output should be the header of the NCBI data page, which looked like this when I ran it:

Last-Modified: Fri, 11 Sep 2020 01:37:40 GMT
Content-Length: 350149451
Accept-ranges: bytes

[Lcornet]

It seems that it comes from my side:

curl ftp://ftp.ncbi.nlm.nih.gov/pub/COG/COG2020/data/cog-20.cog.csv -I
curl: (28) Failed to connect to ftp.ncbi.nlm.nih.gov port 21 after 269607 ms: Couldn't connect to server

Maybe the new version of ubuntu don't allow ftp from terminal for some reasons.

[meren]

Hey @Lcornet, it seem to be a problem on your side as the same command works for me as well.

[Lcornet]

Thanks for quick help, firewall problem.