Resfinder does not show hits as the online platform

[Former user]

Hello,

I have installed and tested Resfinder, and everything seemed to work ok with the test data set (without showing any errors).

Now I have tried to use it with real human metagenomics samples and it does not show any hits (0 hits in the produced report), in contrast to the online website which shows two hits (coverage 60, identity = 90) for acquired antimicrobial resistance genes. I'm not sure what I'm doing wrong.

Here is my example code (I tried this code with and without specifying a path to KMA, in both scenarios no errors were shown): python3 run_resfinder.py -db_res /mnt/d/Metagenomics_trial/resfinder/db_resfinder -k /mnt/d/Metagenomics_trial/resfinder/cge/kma/kma -db_point /mnt/d/Metagenomics_trial/resfinder/db_pointfinder -ifq /mnt/d/trial/Sample_kneaddata_paired_1.fastq /mnt/d/trial/Sample_kneaddata_paired_2.fastq -acq -l 60 -t 90 -o /mnt/d/trial/resfinder

[CGE Helpdesk]

Dear Mr/Ms,

Thank you for the interest in ResFinder.

I don’t know what kind of hit you got in the webpage? Point mutations?

The command line that you have attached does not specify to detect for point mutations. If you would like to detect point mutations, you should specify it with the flag --point and then also a species with the flag --species, e.g. --species “e coli”.

If that does not solve the problem, I will be happy to take a closer look.

If you pass me the link to the result page here: [e-mail] (and then tell us that it is regarding issue #47 in Rescinder), then we can more easily recreate your issue.

Kind regards,

Malene

[mahmoud ismael]

Hello,

Not I do not want to detect point-mutation. My aim is to find acquired ARGs. I have sent you the results page over e-mail. Thanks a lot in advance!

[CGE Helpdesk]

Dear Mahmoud Ismael,

Thank you for re-submitting your job.

By converting the threshold parameters -l and -t from percentages to decimal numbers (-l 0.6 -t 0.9), I was able to reproduce the same results as the CGE webserver.

Best,
Karen, CGE Helpdesk