antismash download databases issue.

Question

[Shakunthala Natarajan]

I am trying to install antismash. After initial set up steps as mentioned in the documentation page, I executed the following command in my pwd to download antismash databases:

python3 download_databases.py

But an error message shows up as:

 OSE error: errno: 28 No space on disk

But I have enough space in the directory in which I was running the antismash installation (around 600 GB)

So when I searched for where the databases have been downloaded, I found them in a hidden folder in my home directory which has very little disk space (~20 GB). The script has hence installed the databases to the home folder by default.

Can someone please let me know how I can change the target location for the antismash databases to get downloaded fully?

Thank you!

Answer 1

[kblin]

The script should install the databases into the database directory. By default, this is in your antiSMASH install location. You can however set this directory to be elsewhere on your computer. The easiest way to do this for both the download script and antiSMASH itself is to create an antiSMASH configuration file in your home directory called .antismash6.cfg containing the line

data /path/to/where/the/database/files/should/live

E.g. for me the line says

data /data/databases/as6

and then that's where all of my database files live:

$ ls -F /data/databases/as6/
clusterblast/  clustercompare/  pfam/  resfam/  tigrfam/

[Shakunthala Natarajan]

I created the file .antismash6.cfg and mentioned the path to the directory for storing the databases and again executed the command

python3 download_databases.py

But this time, I am getting the following error:

ImportError: cannot import name 'Markup' from 'jinja2'

(I didn't get this error while running the script a few days back)

I tried the following fixes:

pip install --upgrade jinja2

Then I tried,

pip install flask==2.0.3

I also tried installing a lower version of jnja2 with

pip install jinja2==3.1.1

Then I did

sudo apt install mailutils

followed by

from jinja2.utils import markupsafe

and it said from: too many arguments

So I am stuck at this place and still not able to download the databases.

Answer 2

[Mensur Dlakic]

I would look into download_databases.py, as it is very likely that directory locations are specified in that script. It is also possible that a temporary download is done in your home directory, after which the database is installed in your present directory.