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 correct 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?