Difficulty downloading databases in humann3

Microbial community profiling HUMAnN
22

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

23

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

24

Hi @szehan,

Apologies for the inconvenience. We had a server outage over the weekend due to which Kneaddata databases downloads was failing.

http://huttenhower.sph.harvard.edu/kneadData_databases/Homo_sapiens_hg37_and_human_contamination_Bowtie2_v0.1.tar.gz

The above link works now.

Regards,
Sagun

1 Like
25

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?

26

Yes, @hshcao You can find it here

27

Thank you very much.
Huansheng

28

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

29

Hello @siraje , I am re-posting the link shared by @fbeghini : Index of /databases/HUMAnN

Thank you!
Lauren

30

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
Siraje

31

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?

Thanks
Nisha

32

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

33

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.

34

For all the 3 database, shall we use the same command to configure?

humann_config --update database_folders nucleotide <path of the database>

35

@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
36

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

37

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!