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]