Metaphlan3 DB won't download for Humann3.6

Microbial community profiling MetaPhlAn
1

Hi all,

I’m trying to test Humann3.6 installed via conda but it looks like it’s trying to download from a broken link:


Error message returned from metaphlan :

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 "/research/bsi/projects/staff_analysis/m141127/conda/biobakery3_2/bin/metaphlan", line 10, in <module>
    sys.exit(main())
  File "/research/bsi/projects/staff_analysis/m141127/conda/biobakery3_2/lib/python3.7/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 "/research/bsi/projects/staff_analysis/m141127/conda/biobakery3_2/lib/python3.7/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

I manually went to that URL and it doesn’t appear to be working. Is there an alternate link we should use, or is it possible to restore the file list to this original location since that’s what the conda install is pointing to?

Thanks!

2

Hi @sjohnson
Humann3.6 needs to work with the latest metaphlan 4 database (is not compatible with metaphlan 3 that should be use with humann versions below 3.5). I suggest you to upgrade your metaphlan installation to the latest version available (4.0.3)

3

Can the conda recipe be upgraded to use metaphlan 4, or at least have this be noted somewhere in the documentation?

4

Hi @sjohnson
If you are doing a fresh installation (no previous metaphlan or humann installation in your conda environment) humann3.6 recipe should automatically install metaphlan 4 (if this is not the case, please report it into the humann subforum HUMAnN - The bioBakery help forum). In case you are upgrading your previous installation, metaphlan should also be manually upgraded. Please have a look at the following guide (it is for 3.5 but works the same for 3.6): Announcing HUMAnN 3.5