SQL error on import

[oliverdrechsel]

Hi,

i installed your tool employing conda.
On Database import i receive a sql error

$ wgmlst import https://www.cgmlst.org/ "Burkholderia pseudomallei"

sqlite3.OperationalError: unable to open database file

[...]
return self.dbapi.connect(*cargs, **cparams)
sqlite3.OperationalError: unable to open database file

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
[...]
return self.dbapi.connect(*cargs, **cparams)
sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) unable to open database file
(Background on this error at: https://sqlalche.me/e/14/e3q8)

Could you help me finding the mistake i do?

cheers.

[bvalot]

Hello,

The database name is the name of the file created in you computer. The command line must be something like this:
$ wgmlst import B.pseudomallei.db "Burkholderia pseudomallei"

And you use this database for the rest of the pipeline in the other command.

Hope it would be clear!
Benoit

[oliverdrechsel]

Hi,

thanks. This worked prefectly fine.

By the way i think there is a small error in the documentation.

# documentation
wgMLST add --help
Usage: wgMLST add [OPTIONS] GENOME DATABASE

In reality GENOME and DATABASE are swapped.

# program help/usage
 $ wgMLST add --help
Usage: wgMLST add [OPTIONS] DATABASE GENOME

[bvalot]

Nice.

You right, I update documentation accordingly.