Error with HUMANnN 3.0 and diamond version

Hello,

I just installed HUMAnN 3.0 and get an error when I try to run it:

CRITICAL ERROR: Please update diamond from version 0.8.22 to version 0.9.24

I check my diamond db info:
$ diamond dbinfo --db uniref90_201901.dmnd
diamond v2.0.4.142 © Max Planck Society for the Advancement of Science
Documentation, support and updates available at http://www.diamondsearch.org

Database format version = 2
Diamond build = 125
Sequences = 87296736
Letters = 29247941583

What do I need to do to fix this?

Thank you,
Sophie

1 Like

Hi Sophie, Thanks for the detailed post. It looks like you might have a diamond version installed that is not compatible with the HUMAnN version. If you would install diamond v0.9.24 it should match the version expected by HUMAnN and resolve the error message.

Thank you,
Lauren

Hello Lauren,

I downgraded to v0.9.24 and I am now getting the error
CRITICAL ERROR: Please update diamond from version 0.8.22 to version 0.9.24

However when I check my diamond version:
$ diamond dbinfo --db uniref90_201901.dmnd
diamond v0.9.24.125 | by Benjamin Buchfink buchfink@gmail.com
Licensed under the GNU GPL https://www.gnu.org/licenses/gpl.txt
Check http://github.com/bbuchfink/diamond for updates.

Database format version = 2
Diamond build = 125
Sequences = 87296736
Letters = 29247941583

Any ideas?

Thanks,
Sophie

Hi Sophie - Thank you for the detailed follow up and sorry you are still seeing the error. Can you run “$ diamond --version” and see what it prints out? If that also lists “v0.9.24” can you double check you don’t have two versions of diamond installed and maybe HUMAnN is selecting the older version? If so you can run HUMAnN with the option “–diamond <full_path_to_directory_with_exe>” to point HUMAnN to the diamond executable that you would like to run with.

Thank you,
Lauren

When I run “$ diamond --version” I get “diamond version 0.9.24”

When I try running humann specifying the path to diamond:
$ ~/anaconda3/envs/biobakery3/bin/humann -i ./merged/d11_1901Seekatz24_12.fa -o ./humann_out --output-basename d11_1901Seekatz24 --diamond ~/anaconda3/envs/biobakery3/bin/diamond

I still get this output:
CRITICAL ERROR: Please update diamond from version 0.8.22 to version 0.9.24

Hello, Thanks for the additional information. Would you try again with the path to the diamond executable folder instead of the full executable path (so use “–diamond ~/anaconda3/envs/biobakery3/bin/”)? Sorry it is a little confusing but HUMAnN expects the folder with the executable instead of the full executable path. If you still see the error I wonder if the diamond version output is slightly different then expected by HUMAnN like is the case for some of the bowtie2 conda installs. If you still see the error after rerunning with the change, if you would post the full contents of running “$ diamond --version” along with how you installed diamond that would be great.

Thank you,
Lauren

Thank you so much for your help, Lauren. Your last suggestion of using “–diamond ~/anaconda3/envs/biobakery3/bin/” is working so far!