Unable to download when running MetaPhlAn3

Microbial community profiling MetaPhlAn
1

Hi,

I am writing to seek assistance with an issue I have encountered while running the metaphlan for provided test dataset on cluster.

MetaPhlAn version 3.0 (25 Feb 2020)

The code I run:
$ metaphlan SRS014476-Supragingival_plaque.fasta.gz --input_type fastq > SRS014476-Supragingival_plaque_profile.txt

The error message I got:
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 “/rsrch6/home/biostatistics/zwang26/.conda/envs/map4-4.0.6/bin/metaphlan”, line 10, in
sys.exit(main())
File “/rsrch6/home/biostatistics/zwang26/.conda/envs/map4-4.0.6/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 “/rsrch6/home/biostatistics/zwang26/.conda/envs/map4-4.0.6/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

Any help is greatly appreciated.
Ziyi

2

http://cmprod1.cibio.unitn.it/biobakery3/metaphlan_databases/

4

Unfortunately, the dropbox download has been deprecated and thus old versions of metaphlan 3 will not be able to automatically download the database. I recommend you to upgrade the metaphlan code to 3.0.14