Hi @luvalli,
After reinstalling Microconda, Qiime2 Amplicon, and ANCOM-BC,
It's possible that the issue here is that you don't need to be installing ANCOM-BC independently of QIIME 2. Could try reinstalling the QIIME 2 amplicon distribution, and then running your qiime composition ancombc command?
To explain why I think this might be the issue: The plugin repository that you're referring to is a third-party plugin that pre-dated the including of ancombc in the QIIME 2 amplicon distribution, so I think the install instructions you're following there might be causing some problems with your QIIME 2 environment. Sorry for the confusion - I'm going to touch base with the developer of that plugin (cc @mortonjt) to see if a note could be added to avoid this confusion in the future.