I have basic question about the use of Metaphlan2 in a standalone computer with no connection to internet. The software is installed in a Mac computer but can it worked without internet? Or internet connection is required to run all the analysis?
I would appreciate the feedback on this. Thank you!
the internet connection is required only for downloading the database. The analysis can be done offline.
Perfect! Thanks so much for the answer!
I was trying to download clade marker database locally by the command:
$ metaphlan2.py --install
My network download speed is not less than at least 1.5MBps. But when I download this particular database, it becomes super slow (around 20kbps). Is it normal or I’m having some issues?
Hi! Hope you are doing well!
I am retaking this topic again. I was not able to work on this due to the pandemic.
So my issue is the following. I was trying the command: metaphlan2.py Natick-WGS-240_R1.fastq --input_type fasta > Natick_WGS_240 (that is the name of the sample I am using as practice) and I was getting this message: metaphla2.py: command not found
I started looking on internet and I found that you could add python at the beginning like this:
python metaphlan2.py Natick-WGS-240_R1.fastq --input_type fasta > Natick_WGS_240
I got this after running that option:
Warning! Biom python library not detected!
Exporting to biom format will not work !
Downloading MetaPhlan2 database
Please note due to the size this might take a few minutes
Warning: Unable to download https://bitbucket.org/biobakery/metaphlan2/downloads/mpa_v20_m200.tar
Warning: Unable to download Downloading https://bitbucket.org/biobakery/metaphlan2/downloads/mpa_v20_m200.md5
File “/Users/ida.pantojafeliciano/Downloads/metaphlan2/metaphalan_databases/mpa_v20_m200.md5” not found!
File “/Users/ida.pantojafeliciano/Downloads/metaphlan2/metaphalan_databases/mpa_v20_m200.tar” not found!
MD5 checksums not found, something went wrong!
I got a folder called “metaphlan_databases” but is empty. So this is the step that requires internet? I checked and I can’t find mpa_v20_m200.tar and mpa_v20_m200.md5 in any place in the computer.
Its a good idea to use “python” at the beginning of the command?
Yes, in order to install the database, an internet connection is required. But first, you should update your MetaPhlAn2 installation, if you have conda installed, you can run
conda install metaphlan2=2.7.8 since the local copy you have is an old build still pointing to the old repo.
Then, you should run
metaphlan2.py --install for downloading and builiding the database.
Thanks so much for your answer. I am guessing that for the conda install command I need the internet connection too, right?
Yes, unfortunately, yes.
To avoid using conda, you can clone the repository from GitHub and manually download the database from here