Metaphlan3.1 database download fails

Microbial community profiling MetaPhlAn
1

Hi,
I am trying to setup metaphlan3.1 and when I try to install the databases it fails because dropbox links do not exist. When I look into the metaphlan.py file it seems like the version downloaded by conda is 3.0
version = ‘3.0’
date = ‘25 Feb 2020’

Here is the command and error it produced
metaphlan --install --bowtie2db /shared/dbs/metaphlan3.1/

Downloading https://www.dropbox.com/sh/7qze7m7g9fe2xjg/AAA4XDP85WHon_eHvztxkamTa/file_list.txt?dl=1

Warning: Unable to download https://www.dropbox.com/sh/7qze7m7g9fe2xjg/AAA4XDP85WHon_eHvztxkamTa/file_list.txt?dl=1
Traceback (most recent call last):
  File "/home/hena.ramay/miniconda3/envs/metaphlan3.1/bin/metaphlan", line 10, in <module>
    sys.exit(main())
  File "/home/hena.ramay/miniconda3/envs/metaphlan3.1/lib/python3.6/site-packages/metaphlan/metaphlan.py", line 1187, in main
    pars['index'] = check_and_install_database(pars['index'], pars['bowtie2db'], pars['bowtie2_build'], pars['nproc'], pars['force_download'])
  File "/home/hena.ramay/miniconda3/envs/metaphlan3.1/lib/python3.6/site-packages/metaphlan/metaphlan.py", line 589, in check_and_install_database
    index = resolve_latest_database(bowtie2_db, ls_f['mpa_latest'], force_redownload_latest)
UnboundLocalError: local variable 'ls_f' referenced before assignment

Thanks for your help in adavance!
Hena

2

Hi @Hena
It seems your version of the MetaPhlAn tool is quite old and it still used the dropbox download that now has been deprecated. I will suggest you to upgrade it with: conda install -c bioconda metaphlan