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AnantharamanLab / VIBRANT

Virus Identification By iteRative ANnoTation
GNU General Public License v3.0
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Issue with KEGG ftp link #77

Open charlesfoster opened 1 year ago

charlesfoster commented 1 year ago

Hi, Just FYI, while trying to set up VIBRANT, I kept getting ftp timeout errors for the KEGG database download.

The link in VIBRANT_setup.py is: ftp://ftp.genome.jp/pub/db/kofam/archives/2019-08-10/profiles.tar.gz. As far as I can tell, the link should (?now) be: https://www.genome.jp/ftp/db/kofam/archives/2019-08-10/profiles.tar.gz.

(I know https vs ftp is one matter, but I think changing '/pub/' to '/ftp/' might be a necessary step?)

The setup python script worked for me after changing the links in the wget 'section' (ll. 70 - 101) to:

http://fileshare.csb.univie.ac.at/vog/vog94/vog.hmm.tar.gz
https://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam32.0/Pfam-A.hmm.gz
https://www.genome.jp/ftp/db/kofam/archives/2019-08-10/profiles.tar.gz

Apologies if this is just a 'me' - posting in case it's useful.

KrisKieft commented 1 year ago

I tested the links and had the same issue. I updated the KEGG and Pfam links. Thank you for pointing this out.

Kris