Database usage error Workflows

Infrastructure and utilities bioBakery workflows
1

Hi to everybody, I installed Biobakery and to get started with it I’m starting to explore MetaPhlAn 3.0.

In order to get a general idea on the interaction with the system before digging into the online tutorials and manuals, I tried to run the example which can be found at MetaPhlAn 3.0 GitHub page:

After downloading the input files present at the same page and following the written steps, I executed the following code

metaphlan SRS014476-Supragingival_plaque.fasta.gz --input_type fasta > SRS014476-Supragingival_plaque_profile.txt

which results in the error:

ERROR: The directory is not writeable: /usr/local/lib/python3.6/dist-packages/metaphlan/metaphlan_databases. Please modify the permissions.

I am using the database mpa_v30_CHOCOPhlAn_201901_marker_info.txt. I did try to modify the permissions with no success in that it was not allowed.
I am using BioBakery on
VirtualBox 7.0.4 r154605
Vagrant 2.3.4
Python 2.7.17, 3.6, 3.8

I also had problems in running the GraPhlAn demo reported at:

with the code

 biobakery_tests --tool graphlan --mode demo --output ~/Desktop/vagrant/

as the terminal returns the error: “biobakery_test command not found”.

I need help mainly to solve the issue with MetaPhlAn as I need to run the simulation before studying the tutorial and manuals to be able to apply the concept into practice and accelerate my learning.
I apologise in advance for the likely basic level of the question, but I am a medical student with no background in Biostatistics but some understanding and basic studies in coding and I.T.
I am learning to use Biobakery because I find it potentially useful in my future possible prosecution of studies and carreer in research after my degree.
Thank you in advance

P.S. I initially posted the same issue in “Microbial community profiling/MetaPhlAn” and I am now posting here under suggestion in a reply to the original post.

2

Hello, Thank you for the detailed post! If you are on the bioBakery VirtualBox you might need to run with “sudo” to change permissions on folders and install the database in the root folder. If you have not used sudo before you just place “sudo” in front of your command and you can think of sudo like “super user do” in that it allows you to run commands with elevated permissions. Alternatively you can select a different install folder for the MetaPhlAn database instead of the root folder: $ metaphlan --install --bowtie2db <database folder> but if you do this also provide the folder location with --bowtie2db <folder> when you run MetaPhlAn. It looks like the second error is it possibly running “biobakery_test” instead of “biobakery_tests”. If this does not fix it then please post again.

Thank you!
Lauren