Different results with LEfSe between Galaxy and Conda

Hello everyone, I’ve noticed a discrepancy between the results from LEfSe on Galaxy and my local LEfSe setup via Conda. Despite using the same input file for both platforms, the outcomes aren’t consistent. While the identified species remain the same, their LDA scores differ, especially for the species highlighted in red. This has led to a change in their rankings. I’ve verified that my local LEfSe version is 1.1.2. Has anyone encountered a similar issue or have insights on how to address this? Furthermore, can I rely on the results from my local LefSe installation?

can you share your build and format script? Unfortunately I can’t help with your question, but I have been trying to get a local version of conda LEfSe installed and have been having a lot of trouble because the format script appears to be out of date. Thank you