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.
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.
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.