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
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.