HUMAnN database download

Microbial community profiling HUMAnN
21

Dear Lauren,

I am using HUMAnN V3.9 and attempted to download the ChocoPhlAn database. I have tried three different methods, but none of them have worked

1

$ humann_databases --download chocophlan full ./
Creating subdirectory to install database: /bac/humann3_reference/v201901_v31/uniref/chocophlan
Download URL: http://huttenhower.sph.harvard.edu/humann_data/chocophlan/full_chocophlan.v201901_v31.tar.gz
CRITICAL ERROR: Unable to download and extract from URL: http://huttenhower.sph.harvard.edu/humann_data/chocophlan/full_chocophlan.v201901_v31.tar.gz

2

wget http://huttenhower.sph.harvard.edu/humann_data/uniprot/uniref_annotated/uniref50_annotated_v201901b_full.tar.gz
--2024-07-22 15:06:57--  http://huttenhower.sph.harvard.edu/humann_data/uniprot/uniref_annotated/uniref50_annotated_v201901b_full.tar.gz
Resolving huttenhower.sph.harvard.edu (huttenhower.sph.harvard.edu)... 199.94.60.28
Connecting to huttenhower.sph.harvard.edu (huttenhower.sph.harvard.edu)|199.94.60.28|:80... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://huttenhower.sph.harvard.edu/humann_data/uniprot/uniref_annotated/uniref50_annotated_v201901b_full.tar.gz [following]
--2024-07-22 15:06:57--  https://huttenhower.sph.harvard.edu/humann_data/uniprot/uniref_annotated/uniref50_annotated_v201901b_full.tar.gz
Connecting to huttenhower.sph.harvard.edu (huttenhower.sph.harvard.edu)|199.94.60.28|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://g-227ca.190ebd.75bc.data.globus.org/humann_data/uniprot/uniref_annotated/uniref50_annotated_v201901b_full.tar.gz [following]
--2024-07-22 15:06:58--  https://g-227ca.190ebd.75bc.data.globus.org/humann_data/uniprot/uniref_annotated/uniref50_annotated_v201901b_full.tar.gz
Resolving g-227ca.190ebd.75bc.data.globus.org (g-227ca.190ebd.75bc.data.globus.org)... 140.247.111.39, 140.247.111.40
Connecting to g-227ca.190ebd.75bc.data.globus.org (g-227ca.190ebd.75bc.data.globus.org)|140.247.111.39|:443... failed: Connection refused.
Connecting to g-227ca.190ebd.75bc.data.globus.org (g-227ca.190ebd.75bc.data.globus.org)|140.247.111.40|:443... failed: Connection refused.

3
https://g-227ca.190ebd.75bc.data.globus.org/
ERR_CONNECTION_CLOSED

Best wishes,
Pofive

22

Hello all,

Have receive this message when downloading the DB:
Connecting to g-227ca.190ebd.75bc.data.globus.org (g-227ca.190ebd.75bc.data.globus.org)|140.247.111.39|:443… failed: Connection refused

wget https://huttenhower.sph.harvard.edu/humann_data/uniprot/uniref_annotated/uniref90_annotated_v201901b_full.tar.gz

https://huttenhower.sph.harvard.edu/humann_data/chocophlan/full_chocophlan.v201901_v31.tar.gz

1 Like
23

Hi,
I encountered the same problem, regarding downloading the humann database using humann_download command and wget <URLs https://huttenhower.sph.harvard.edu/ displayed during --available>.
The URL gets connected but the script ran for days on the cluster but nothing gets downloaded nor the script exits with an error.
Tool info: humann v3.9 [Conda installed in a new environment]
Finally Lauren’s solution to download via their Globus servers.

[quote=“lauren.j.mciver, post:18, topic:6690”]
wget https://g-227ca.190ebd.75bc.data.globus.org/humann_data/chocophlan/full_chocophlan.v201901_v31.tar.gz
[/quote]

24

–2024-12-03 12:18:04-- (try:20) https://g-227ca.190ebd.75bc.data.globus.org/humann_data/chocophlan/full_chocophlan.v201901_v31.tar.gz

Connecting to g-227ca.190ebd.75bc.data.globus.org (g-227ca.190ebd.75bc.data.globus.org)|140.247.111.39|:443… failed: Operation timed out.

Connecting to g-227ca.190ebd.75bc.data.globus.org (g-227ca.190ebd.75bc.data.globus.org)|140.247.111.40|:443… failed: Operation timed out.

Giving up.

Still getting the download error is there a solution to this or give up on this develop something else?

1 Like
25

I’m using humann v4.0.0.alpha.1. I’m also getting a similar problem except I was able to download the full chocophlan database. It’s my first time downloading the uniref90 full database using this version. When I list the available databases for download using “humann_databases --available”, I get the following message:

HUMAnN Databases ( database : build = location )
chocophlan : full = http://huttenhower.sph.harvard.edu/humann_data/chocophlan/chocophlan.v4_alpha.tar.gz
chocophlan : ec_filtered = http://huttenhower.sph.harvard.edu/humann_data/chocophlan/chocophlan_EC_FILTERED.v4_alpha.tar.gz
uniref : uniref90_ec_filtered_diamond = http://huttenhower.sph.harvard.edu/humann_data/uniprot/uniref_ec_filtered/uniref90_annotated_v4_alpha_ec_filtered.tar.gz
utility_mapping : full = http://huttenhower.sph.harvard.edu/humann_data/full_mapping_v4_alpha.tar.gz

What I need is the uniref90 full database, but it seems that none of the URLs are working as I’ve tried using wget on other user’s posts. Any advice would be appreciated!

Thank you.

26

As discussed here in the HUMAnN 4 alpha release notes, we haven’t yet released a comprehensive (“full”) translated protein database for this version as there are still some technical issues to sort out there.

27

This has been happening to me (June 2026) and I am not sure what the issue is. I haven’t had a problem downloading these files previously…would anyone in the biobakery team know why this is failing??

2 Likes
28

Hi all,

I’m unable to download the ChocoPhlAn and Uniref databases and am hitting a consistent connection failure that suggests possibly an issue on the Globus/Harvard side of things?
I ran this:

humann_databases --download chocophlan full /path/to/databases --update-config no

And got this error:

Download URL: http://huttenhower.sph.harvard.edu/humann_data/chocophlan/full_chocophlan.v201901_v31.tar.gz
CRITICAL ERROR: Unable to download and extract from URL: http://huttenhower.sph.harvard.edu/humann_data/chocophlan/full_chocophlan.v201901_v31.tar.gz

I’ve tried it from my institution’s HPC and from my macbook terminal and get the same error from both, so I don’t think it’s a firewall/proxy issue.

Any help would be greatly appreciate, thank you! Happy to provide more info as well.