Access to prebuild databases

[Ales-ibt]

hello!

Thank you for developing SHOGUN, I want to run the tool with the pre-build databases but it looks like the URLs in the shogun_db_links.txt file are outdated. Is there somewhere else I can download the databases from?

This is the message I am getting:

$ wget -i shogun_db_links.txt
--2024-04-23 12:05:44--  http://metagenome.cs.umn.edu/public/shogun-db/metadata.yaml
Resolving metagenome.cs.umn.edu (metagenome.cs.umn.edu)... 128.101.96.204
Connecting to metagenome.cs.umn.edu (metagenome.cs.umn.edu)|128.101.96.204|:80... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: https://knightslab.orgpublic/shogun-db/metadata.yaml [following]
--2024-04-23 12:05:44--  https://knightslab.orgpublic/shogun-db/metadata.yaml
Resolving knightslab.orgpublic (knightslab.orgpublic)... failed: Name or service not known.
wget: unable to resolve host address ‘knightslab.orgpublic’
--2024-04-23 12:05:59--  http://metagenome.cs.umn.edu/public/shogun-db/rep82.fna
Connecting to metagenome.cs.umn.edu (metagenome.cs.umn.edu)|128.101.96.204|:80... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: https://knightslab.orgpublic/shogun-db/rep82.fna [following]
--2024-04-23 12:06:00--  https://knightslab.orgpublic/shogun-db/rep82.fna
Resolving knightslab.orgpublic (knightslab.orgpublic)... failed: Name or service not known.
wget: unable to resolve host address ‘knightslab.orgpublic’
--2024-04-23 12:06:10--  http://metagenome.cs.umn.edu/public/shogun-db/rep82.tax
Reusing existing connection to metagenome.cs.umn.edu:80.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: https://knightslab.orgpublic/shogun-db/rep82.tax [following]
--2024-04-23 12:06:10--  https://knightslab.orgpublic/shogun-db/rep82.tax
Resolving knightslab.orgpublic (knightslab.orgpublic)... failed: Name or service not known.
wget: unable to resolve host address ‘knightslab.orgpublic’
--2024-04-23 12:06:20--  http://metagenome.cs.umn.edu/public/shogun-db/sheared_bayes.txt
Reusing existing connection to metagenome.cs.umn.edu:80.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: https://knightslab.orgpublic/shogun-db/sheared_bayes.txt [following]
--2024-04-23 12:06:20--  https://knightslab.orgpublic/shogun-db/sheared_bayes.txt
Resolving knightslab.orgpublic (knightslab.orgpublic)... failed: Name or service not known.
wget: unable to resolve host address ‘knightslab.orgpublic’
--2024-04-23 12:06:30--  http://metagenome.cs.umn.edu/public/shogun-db/utree/rep82.gg.ctr
Reusing existing connection to metagenome.cs.umn.edu:80.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: https://knightslab.orgpublic/shogun-db/utree/rep82.gg.ctr [following]
--2024-04-23 12:06:30--  https://knightslab.orgpublic/shogun-db/utree/rep82.gg.ctr
Resolving knightslab.orgpublic (knightslab.orgpublic)... failed: Name or service not known.
wget: unable to resolve host address ‘knightslab.orgpublic’
--2024-04-23 12:06:40--  http://metagenome.cs.umn.edu/public/shogun-db/utree/rep82.gg.log
Reusing existing connection to metagenome.cs.umn.edu:80.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: https://knightslab.orgpublic/shogun-db/utree/rep82.gg.log [following]
--2024-04-23 12:06:40--  https://knightslab.orgpublic/shogun-db/utree/rep82.gg.log
Resolving knightslab.orgpublic (knightslab.orgpublic)... 

Thanks in advance!

[bhillmann]

Hello, we are currently looking to track them down since our links went down. Hopefully, the files will be back up soon!

[Ales-ibt]

Brilliant! Thank you so much for your quick reply.

[Ales-ibt]

Hello! Any updates about this?

[bhillmann]

We haven't made any positive progress on this yet. Sorry about the delay, I don't have access to my old labs storage but am in contact to try and get copies of those files and get them rehosted.

[Ales-ibt]

Thank you so much, I hope the matter can be solved soon. Bests.

[Ashma45]

Following

[danknights]

I/T issue. Fixed and above links now are working.

[danknights]

OK fixed now

On Tue, Apr 23, 2024 at 12:16 PM Benjamin Hillmann @.***> wrote:

Assigned #46 https://github.com/knights-lab/SHOGUN/issues/46 to @danknights https://github.com/danknights.

— Reply to this email directly, view it on GitHub https://github.com/knights-lab/SHOGUN/issues/46#event-12579012292, or unsubscribe https://github.com/notifications/unsubscribe-auth/AATPLY5LR2ITI7IEKTWHDB3Y62JPPAVCNFSM6AAAAABGUVUQ52VHI2DSMVQWIX3LMV45UABCJFZXG5LFIV3GK3TUJZXXI2LGNFRWC5DJN5XDWMJSGU3TSMBRGIZDSMQ . You are receiving this because you were assigned.Message ID: @.***>

[Ales-ibt]

Thank you! I can confirm I had successfully downloaded the DBs