CRITICAL ERROR: Unable to find the MetaPhlAn python package. Please check your install

Microbial community profiling MetaPhlAn
1

Greetings,
I am using Metaphlan v4.1.1 and trying to customize the database using my genomes (I want to run metagenomics data against the collection of genomes from my isolates). I have used the method described here.

  • My new_marker.fasta file contains sequences from all the genomes.

  • The last part of the tutorial asks to run metaphlan.py with the “–index mpa_vJun23_CHOCOPhlAnSGB_NEW” parameter. Following that, I got this error
    CRITICAL ERROR: Unable to find the MetaPhlAn python package. Please check your install. using the command metaphlan.py --index mpa_vJun23_CHOCOPhlAnSGB_NEW

The new database is in a different directory than installation directory, also metaphlan.py is present in /usr/mpa/lib/python3.7/site-packages/metaphlan
Please let me know how to resolve this issue.

Second, I have 11 species of Enterococcus in my genomes, out of which nine I found in the database; two of them (E. lactis and E. entomosocium) are not there. How could I add them to the database?

FYI, I have attached taxonomy file.
taxonomy-file-python.txt (19.0 KB)

Please let me know if you need any other information.

Thank you.