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ncbi / amr

AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.
https://www.ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/AMRFinder/
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amrfinder running with options --ident_min and --coverage_min #126

Closed stalact closed 1 month ago

stalact commented 1 year ago

Hi all, I want to run amrfinder with minimum identity of 80% and a coverage of 90%:

Running: amrfinder -n genome.fna --ident_min 0.8 --coverage_min 0.9 -o genome.tsv

A gene listed with 55% Identity to reference sequence. Are the arguments passed properly? This gene should not be listed, since the minimum should be 80% identy? The same issue occurs with the protein option.

Thanks for your help :-)

vbrover commented 1 year ago

Could you post genome.fna?

evolarjun commented 1 month ago

Resolving since we don't have test data. Please reopen and include test data if this is still an issue.