plasmidfinder the specified database directory does not exist! (due to an extra comma)

[dadrasarmin]

Hi,

there was a report that a user cannot use plasmidfinder on usegalaxy.eu with the built-in database called: "81c11f4_2023_12_04". I could reproduce the error here. I believe it is because of the extra comma (81c11f4_2023_12_04,/data) in the submitted command:

mkdir output_dir && mkdir temp_dir && plasmidfinder.py -i '/data/dnb10/galaxy_db/files/7/0/c/dataset_70c9bbbd-7907-43d2-ac0b-b827bca736f1.dat' -p '/data/db/data_managers/plasmidfinder-db/81c11f4_2023_12_04,/data/db/data_managers/plasmidfinder-db/81c11f4_2023_12_04' -l '0.6' -t '0.95' -mp blastn -x -o output_dir -tmp temp_dir | tee 'XXXX'

the same input fasta file will successfully work with the "2.1_2019_08_28" database. As attached below we can also see that the 2023 database is available twice as an option which I believe is also for that extra comma.

I looked into the xml files but could not figure out were these information has been coded. I appreciate if someone can help.

[bgruening]

please try again.

[dadrasarmin]

It works and finishes successfully. Thanks.

[wennj]

Now the tool is still aborting with the following error message:

Fatal error:
Error: KMA did not run as expected.
KMA finished with the following response:

Filename: /data/db/data_managers/plasmidfinder-db/81c11f4_2023_12_04/enterobacteriales.length.b
Error: 2 (No such file or directory)

https://usegalaxy.eu/u/wennmannj/h/plasmidfinder-error

[SaimMomin12]

@bgruening Looks like there are some missing files in the plasmidfinder db causing the error

[bgruening]

Yes, but why and how should such a directory look like....

[bgruening]

Or does the tool tries to write into this directory and this is why we get this error ...