The bioBakery help forum

Md5 sums for humann2_data databases

I am trying to download the databases from http://huttenhower.sph.harvard.edu/humann2_data/uniprot/uniref_annotated/uniref90_annotated_v201901.tar.gz
and
http://huttenhower.sph.harvard.edu/humann2_data/chocophlan/full_chocophlan.v296_201901.tar.gz

These are both databases over 15GB in size. I frequently have difficulties with downloading large files and I’d like to ensure the integrity of the files.

Question :

  1. Where would I find the md5 sums or other check sums for these files?

Me, too. It’s also disappointing that humann_databases doesn’t support resuming broken downloads. It repeatedly fails after about 80% to 90% of ChocoPhlAn is downloaded.

(Python3) /verona/biostat/databases/bacteria$ humann_databases --download chocophlan full /verona/biostat/databases/bacteria/                                                                                 Download URL: http://huttenhower.sph.harvard.edu/humann_data/chocophlan/full_chocophlan.v296_201901b.tar.gz
Downloading file of size: 16.01 GB

CRITICAL ERROR: Unable to download and extract from URL: http://huttenhower.sph.harvard.edu/humann_data/chocophlan/full_chocophlan.v296_201901b.tar.gz
(Python3) /verona/biostat/databases/bacteria$ ls -lht full_chocophlan.v296_201901b.tar.gz
-rw-r----- 1 biostat biostat 13G May 21 17:06 full_chocophlan.v296_201901b.tar.gz

(Python3) /verona/biostat/databases/bacteria$ humann_databases --download chocophlan full /verona/biostat/databases/bacteria/
Download URL: http://huttenhower.sph.harvard.edu/humann_data/chocophlan/full_chocophlan.v296_201901b.tar.gz
Downloading file of size: 16.01 GB

CRITICAL ERROR: Unable to download and extract from URL: http://huttenhower.sph.harvard.edu/humann_data/chocophlan/full_chocophlan.v296_201901b.tar.gz
(Python3) /verona/biostat/databases/bacteria$ ls -lht full_chocophlan.v296_201901b.tar.gz
-rwxrwx--- 1 biostat biostat 14G May 22 01:54 full_chocophlan.v296_201901b.tar.gz

I am located in Australia, which is far from anywhere else and download speed is about 0.65 MB/s.