[Errno2] | Run a single sample

Microbial community profiling MetaPhlAn
1

Hello!
I’m trying to run this command to run a single sample for an eDNA sample, from whole genome shotgun sequencing, with MetaPhlAn3.0 based on the Biobakery Wiki page, but I get the following error. Would you please help me to troubleshoot it? Thanks!

metaphlan July142020-1996A1_S35_L001_R1_001.fastq.gz --input_type fastq > July142020-1996A1_S35_L001_R1_001_profile.txt

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

Warning: Unable to download http://cmprod1.cibio.unitn.it/biobakery3/metaphlan_databases/mpa_latest
Traceback (most recent call last):
File “/usr/local/bin/metaphlan”, line 8, in
sys.exit(main())
File “/usr/local/lib/python3.6/dist-packages/metaphlan/metaphlan.py”, line 985, in main
pars[‘index’] = check_and_install_database(pars[‘index’], pars[‘bowtie2db’], pars[‘bowtie2_build’], pars[‘nproc’], pars[‘force_download’])
File “/usr/local/lib/python3.6/dist-packages/metaphlan/init.py”, line 283, in check_and_install_database
index = resolve_latest_database(bowtie2_db, mpa_latest, force_redownload_latest)
File “/usr/local/lib/python3.6/dist-packages/metaphlan/init.py”, line 244, in resolve_latest_database
with open(os.path.join(bowtie2_db,‘mpa_latest’)) as mpa_latest:
FileNotFoundError: [Errno 2] No such file or directory: ‘/usr/local/lib/python3.6/dist-packages/metaphlan/metaphlan_databases/mpa_latest’

2

It seems that you cannot download the database. Can you access through a web browser to the mentioned URL? Otherwise, you can download the database from Dropbox (https://www.dropbox.com/sh/7qze7m7g9fe2xjg/AADHWzATSQcI0CNFD0sk7MAga)

3

So, even though this is an old thread…I still thought I would post a possible fix for this, as I also struggled quite a bit with a similar error.
Also the link @fbeghini posted seems to be broken(?).

The easiest way I found was to cp mpa_previous as mpa_latest:

cp /your/path/to/miniconda3/envs/humann/lib/python3.7/site-packages/metaphlan/metaphlan_databases/mpa_previous /your/path/to/miniconda3/envs/humann/lib/python3.7/site-packages/metaphlan/metaphlan_databases/mpa_latest

Obviously replace /your/path/to/ with your own correct path. This should resolve the issue so that it won’t be trying to download (which in my case was not working).
The “previous” database is from what I have found still the “latest” anyway (201901). Also I actually find this better, since I would not like it to be downloading newer databases every time I run Humman3 without notifying me, since it would interefere with the reproducibility imo.