# Database usage error

**URL:** <https://forum.biobakery.org/t/database-usage-error/4976>\
**Category:** MetaPhlAn\
**Created:** [March 15, 2023, 7:15pm UTC](https://forum.biobakery.org/t/database-usage-error/4976 "2023-03-15T19:15:08Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![PasqualeD](https://avatars.discourse-cdn.com/v4/letter/p/bc79bd/32.png) [@PasqualeD](https://forum.biobakery.org/u/PasqualeD)\
**Post date:** [March 15, 2023, 7:15pm UTC](https://forum.biobakery.org/t/database-usage-error/4976/1 "2023-03-15T19:15:08Z")

</div>

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:

> **[metaphlan3](https://github.com/biobakery/biobakery/wiki/metaphlan3#overview)**
>
> bioBakery tools for meta'omic profiling. Contribute to biobakery/biobakery development by creating an account on GitHub.

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

```auto
 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:

> **[biobakery\_basic](https://github.com/biobakery/biobakery/wiki/biobakery_basic)**
>
> bioBakery tools for meta'omic profiling. Contribute to biobakery/biobakery development by creating an account on GitHub.

with the code

```auto
 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

---

<div class="post-metadata">

**Author:** ![aitor.blancomiguez](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/aitor.blancomiguez/32/86_2.png) [@aitor.blancomiguez](https://forum.biobakery.org/u/aitor.blancomiguez)\
**Post date:** [March 23, 2023, 8:47am UTC](https://forum.biobakery.org/t/database-usage-error/4976/2 "2023-03-23T08:47:04Z")

</div>

Hi @PasqualeD  
Since the problem seems to be related to the full biobakery suit, could you replicate the post in the following subforum? [bioBakery workflows - The bioBakery help forum](https://forum.biobakery.org/c/infrastructure-and-utilities/biobakery-workflows/11) I think they will better address your problem there

---

<div class="post-metadata">

**Author:** ![PasqualeD](https://avatars.discourse-cdn.com/v4/letter/p/bc79bd/32.png) [@PasqualeD](https://forum.biobakery.org/u/PasqualeD)\
**Post date:** [March 25, 2023, 2:06pm UTC](https://forum.biobakery.org/t/database-usage-error/4976/3 "2023-03-25T14:06:55Z")

</div>

I surely will, thank you very much. Should I delete this post in this subforum?