The bioBakery help forum

[Errno2] | Run a single sample

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


Warning: Unable to download
Traceback (most recent call last):
File “/usr/local/bin/metaphlan”, line 8, in
File “/usr/local/lib/python3.6/dist-packages/metaphlan/”, 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/”, 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/”, 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’

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 (