Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[BUG] Internet and permission issues when connecting to metaphlan online database through proxy server #220

Closed
LMM716 opened this issue Nov 22, 2023 · 1 comment

Comments

@LMM716
Copy link

LMM716 commented Nov 22, 2023

When running MetaPhlAn version 3.0.9 through a proxy server, I get the following errors and warnings:

In the output.txt file:
WARNING: It seems that you do not have Internet access.
WARNING: Cannot connect to the database server. The latest available local database will be used.

in the .err file:
CTraceback (most recent call last):
File "/gpfs/ts0/shared/software/MetaPhlAn/3.0.9-foss-2020a-Python-3.8.2/bin/metaphlan", line 8, in
sys.exit(main())
File "/gpfs/ts0/shared/software/MetaPhlAn/3.0.9-foss-2020a-Python-3.8.2/lib/python3.8/site-packages/metaphlan/metaphlan.py", line 926, in main
pars['index'] = check_and_install_database(pars['index'], pars['bowtie2db'], pars['bowtie2_build'], pars['nproc'], pars['force_download'])
File "/gpfs/ts0/shared/software/MetaPhlAn/3.0.9-foss-2020a-Python-3.8.2/lib/python3.8/site-packages/metaphlan/init.py", line 280, in check_and_install_database
index = resolve_latest_database(bowtie2_db, mpa_latest, force_redownload_latest)
File "/gpfs/ts0/shared/software/MetaPhlAn/3.0.9-foss-2020a-Python-3.8.2/lib/python3.8/site-packages/metaphlan/init.py", line 235, in resolve_latest_database
os.rename(os.path.join(bowtie2_db,'mpa_latest'),os.path.join(bowtie2_db,'mpa_previous'))
PermissionError: [Errno 13] Permission denied: '/gpfs/ts0/shared/software/MetaPhlAn/3.0.9-foss-2020a-Python-3.8.2/lib/python3.8/site-packages/metaphlan/metaphlan_databases/mpa_latest' -> '/gpfs/ts0/shared/software/MetaPhlAn/3.0.9-foss-2020a-Python-3.8.2/lib/python3.8/site-packages/metaphlan/metaphlan_databases/mpa_previous'

I am running on the following:
CentOS Linux release 7.9.2009 (Core)
Linux 3.10.0-1160.92.1.el7.x86_64 x86_64�

I run the following command on an individual file: metaphlan [inputfilename].fastq --input_type fastq > [outputfilename]_output_profile.txt

If possible, I would like to know the URL for database that we are meant to connect to. at the moment we are trying to connect to
http://cmprod1.cibio.unitn.it/ is this correct?

Is there any additional settings we need to apply to make the command work via a proxy server?

Copy link

Thank you for creating this issue.
We currently field issues through our bioBakery Discourse Support Forum.
If you would please post the issue to discourse we would be happy to sync up with you to get it resolved.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant