I’m sorry, but unfortunately I do not have a local copy of that database.
Apologies for the inconvenience. We had a server outage over the weekend due to which Kneaddata databases downloads was failing.
The above link works now.
I installed Humann3 and used the database full_chocophlan.v296_201901.tar.gz and got this error
CRITICAL ERROR: The directory provided for ChocoPhlAn contains files ( full_chocophlan.v296_201901.tar.gz ) that are not of the expected version. Please install the latest version of the database: 201901b
the 201901b differs from 201901 version in header information I guess.
@fbeghini could you share the 201901b database in Dropbox?
Yes, @hshcao You can find it here
Thank you very much.
Hi Would you be able to share the latest uniref90 version 201901b? I have been trying to download from humann website for last three days with no luck. Thanks
Hello @siraje , I am re-posting the link shared by @fbeghini : Index of /databases/HUMAnN
Thanks a lot Lauren for the link. I already tried with this link. However, the download fails after few hours. Therefore I was asking @fbeghini the alternative dropbox link for the latest uniref90 version 201901b. Can you please share that?
any luck in downloading the latest version of Uniref90 and chocophlan? If Yes, could you please provide dropbox links, as I’m also facing a similar issue?
I have already tried this, downloading speed is too slow. now it is 1-2kb/s. and estimated time for complete download is 170 d and still increasing.
For all the 3 database, shall we use the same command to configure?
humann_config --update database_folders nucleotide <path of the database>
@lauren.j.mciver I would like to +1 Claire’s question! Looking at the default output of
humann_config, it seems to suggest chocophlan is the database for which you’d use
... --update ... nucleotide and uniref is the one for which you’d use
... --update ... protein.
The part of my output to which I’m referring is:
HUMAnN Configuration ( Section : Name = Value )
database_folders : nucleotide = /opt/software/mamba_humann/lib/python3.10/site-packages/humann/data/chocophlan_DEMO
database_folders : protein = /opt/software/mamba_humann/lib/python3.10/site-packages/humann/data/uniref_DEMO
database_folders : utility_mapping = /opt/software/mamba_humann/lib/python3.10/site-packages/humann/data/misc
Can anyone please put the full_chocophlan.v201901_v31.tar.gz and UniRef90 database into dropbox? It is not downloading through normal way. It is showing CRITICAL ERROR: Unable to download and extract from URL: http://huttenhower.sph.harvard.edu/humann_data/chocophlan/full_chocophlan.v201901_v31.tar.gz