Difficulty downloading databases in humann3

The links are great!
Could we request for mirror links for Kneaddata database as well?
Link is currently down.

Download URL: http://huttenhower.sph.harvard.edu/kneadData_databases/Homo_sapiens_hg37_and_human_contamination_Bowtie2_v0.1.tar.gz
CRITICAL ERROR: Unable to download and extract from URL: http://huttenhower.sph.harvard.edu/kneadData_databases/Homo_sapiens_hg37_and_human_contamination_Bowtie2_v0.1.tar.gz

I’m sorry, but unfortunately I do not have a local copy of that database.

Hi @szehan,

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.


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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

Thank you!

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?

Thank you

Hi @siraje
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?


wget worked for me. Try this:
wget -c http://huttenhower.sph.harvard.edu/humann_data/uniprot/uniref_annotated/uniref90_annotated_v201901b_full.tar.gz

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

Hello! Were you able to download full_chocophlan.v201901_v31.tar.gz? I’m trying to do it as well but no luck so far. Any help would be greatly appreciate. Thank you!