Internet connection?

Microbial community profiling MetaPhlAn
1

Hi all!

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!
idapantoja

2

Hi,
the internet connection is required only for downloading the database. The analysis can be done offline.

3

Hi,

Perfect! Thanks so much for the answer!

4

Hi Fransesco,
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?

5

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

Downloading https://bitbucket.org/biobakery/metaphlan2/downloads/mpa_v20_m200.tar

Warning: Unable to download https://bitbucket.org/biobakery/metaphlan2/downloads/mpa_v20_m200.tar

Downloading https://bitbucket.org/biobakery/metaphlan2/downloads/mpa_v20_m200.md5

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?

Thank you!
Ida

6

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.

7

Hi @fbeghini,

Thanks so much for your answer. I am guessing that for the conda install command I need the internet connection too, right?

Best regards!
@idapantoja

8

Yes, unfortunately, yes.
To avoid using conda, you can clone the repository from GitHub and manually download the database from here