I am currently running throuh the Metaphlan3 wiki tutorial (https://github.com/biobakery/biobakery/wiki/metaphlan3) with the example data as well as own data. When it comes to creating Graphlan input files with export2graphlan.py I receive tracebacks:
I get this kind of traceback no matter which data I use. When I only install Graphlan and Metaphlan3, the command export2graphlan.py can not be found. Therefore I searched and found the export2graphlan package in bioconda. Running export2graphlan in an environment where the respective package is installed I am getting the traceback shown above.
I use Ubuntu 20.04 and installed each tool in an own environment using conda. I also tried installing different packages in one environment (e. g. Metaphlan and Graphlan, Metaphlan and Graphlan and export2graphlan) but I can not solve the traceback.