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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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No POINT results in combine PROT+NUCL mode #134

Closed bvalot closed 9 months ago

bvalot commented 9 months ago

Hi,

I have a strange results with amrfinderplus. When I use only nucleotide input, I get POINT mutation results. When I make combine mode -n -p -g with nucleotide and protein, the POINT mutations disappear on the results for the same input.

Do I miss some options?

Thanks in advance Benoit

Software version: 3.11.26 Database version: 2023-11-15.1

vbrover commented 9 months ago

Please post complete command lines and the input files.

bvalot commented 9 months ago

amrfinder -d ~/database/amrfinder/latest -n assembly/E118_S138.fna -O Escherichia -o amrfinder/E118_S138

amrfinder -d ~/database/amrfinder/latest -n assembly/E118_S138.fna -O Pseudomonas_aeruginosa -p annotation/E118_S138_ok.faa -g annotation/E118_S138_ok.gff -o amrfinder/E118_S138_combi

bvalot commented 9 months ago

Ah! Sorry. Just see that I use bad -O options...

vbrover commented 9 months ago

Point mutations are species-specific. What is the species of the assembly E118_S138?

bvalot commented 9 months ago

It is Escherichia coli. Just make error on copy/paste :)