I was using my qiime2-amplicon-2025.10 environment normally and wanted to install deicode to create an Aitchison matrix with a robust CLR. However, I started having problems, and from that point on, my conda broke and I couldn't use it anymore. I had to remove the environment and reinstall it. When I do, I get the following error:
ERROR conda.core.link:_execute(1033): An error occurred while installing package 'bioconda::bioconductor-genomeinfodbdata-1.2.11-r43hdfd78a'
I already tried installing it using a YAML file without that package (genomeinfodbdata-1.2.11), and it still doesn't work. Could you give me some advice? I've already read some topics here on the forum, but I haven't found any answers.
Deicode is not compatible with new qiime2 environments. I don’t remember the last version of qiime2 it works with, but it should work with qiime2 2019.1
There is an alternative named GEMELLI, which works with Qiime2 2023.9 or older versions.
If you work in qiime2 2025.10 or newer, you can still install older version in parallel to it. But older qiime2 versions will not recognise your feature table created with latest versions of Q2. So you need to export your feature table as a biom file in Qiime2 2025.10, switch environment to an older Qiime2 version with deicode or gemelli, import the biom file back to Qiime, and calculate robust Aitchison distances with CLR. Then you can switch back to your newer version of qiime2 to proceed with the rest of analyses.