Humann ERROR: Metaphlan is trying to edit the database folder directly

Microbial community profiling HUMAnN
1 
 Error message returned from metaphlan :
Traceback (most recent call last):
  File "/u/local/apps/anaconda3/2020.11/envs/biobakery3/bin/metaphlan", line 10, in <module>
    sys.exit(main())
  File "/u/local/apps/anaconda3/2020.11/envs/biobakery3/lib/python3.7/site-packages/metaphlan/metaphlan.py", line 996, in main
    pars['index'] = check_and_install_database(pars['index'], pars['bowtie2db'], pars['bowtie2_build'], pars['nproc'], pars['force_download'], pars['offline'])
  File "/u/local/apps/anaconda3/2020.11/envs/biobakery3/lib/python3.7/site-packages/metaphlan/__init__.py", line 303, in check_and_install_database
    index = resolve_latest_database(bowtie2_db, mpa_latest, force_redownload_latest, offline)
  File "/u/local/apps/anaconda3/2020.11/envs/biobakery3/lib/python3.7/site-packages/metaphlan/__init__.py", line 258, in resolve_latest_database
    os.rename(os.path.join(bowtie2_db,'mpa_latest'),os.path.join(bowtie2_db,'mpa_previous'))
PermissionError: [Errno 13] Permission denied: '/u/local/apps/anaconda3/2020.11/envs/biobakery3/lib/python3.7/site-packages/metaphlan/metaphlan_databases/mpa_latest' -> '/u/local/apps/anaconda3/2020.11/envs/biobakery3/lib/python3.7/site-packages/metaphlan/metaphlan_databases/mpa_previous'

Something seems off, is it versioning ?

2

If you add --offline to the HUMAnN call to MetaPhlAn it should resolve this issue. I think we have other threads about this if you search for “offline.”