Input Error: Provided database was not recognised!

[Jeevan Karloss]

Not sure what the problem is.

[CGE Helpdesk]

Dear Jeevan Karloos,

Thank you for the interest in our services.

Could please you explain in further detail what the problem is and where it appears? Do you have a command-line example or maybe a screenshot showing where the issue is?

Then I will do my best to try and help you.

Kind regards,

Malene

CGE Helpdesk.

[Jeevan Karloss]

Sorry, It resolved. I am not sure how to use fastq (both reads) files in ResFinder?

[Jeevan Karloss]

I am getting this “Error: (CArgException::eInvalidArg) Unknown argument: "t_db"“ while using fastq files.

[CGE Helpdesk]

Could you please provide me with the command-line that you used when you received this error?

Kind regards,

Malene

CGE helpdesk

[Jeevan Karloss]

Here is the command line I used for FastQ files.
python3 resfinder/resfinder.py -i R1_001.fastq R2_001.fastq -o . -p /resfinder_db -mp ResPoint-finder/bin/blastn

[Jeevan Karloss]

How does ResFinder map reads to Resistance genes? as Raw reads or building genome and map?

[CGE Helpdesk]

It does not look like there is anything wrong with your command line. I would suggest, that you try to upload the data to our web server application here: https://cge.cbs.dtu.dk/services/ResFinder/ . Here you can also find the link to the paper describing the program in more detail: https://cge.cbs.dtu.dk/services/ResFinder/abstract.php.

When you receive the link to the result page you can send us the result link here: [e-mail]. Then it is easier for us to recreate the problem.

Kind regards,

Malene, CGE Helpdesk.