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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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Invalid organism: Burkholderia_mallei #153

Closed Danderson123 closed 1 week ago

Danderson123 commented 1 week ago

Hello, I am running AMRFinderPlus on a large dataset that includes some Burkholderia mallei samples. I specified --organism Burkholderia_mallei for these samples, assuming the supported species were in line with this table https://github.com/ncbi/amr/wiki/Running-AMRFinderPlus#--organism-option, and AMRFinderPlus returned:

*** ERROR ***
Possible organisms: Acinetobacter_baumannii, Burkholderia_cepacia, Burkholderia_pseudomallei, Campylobacter, Citrobacter_freundii, Clostridioides_difficile, Enterobacter_asburiae, Enterobacter_cloacae, Enterococcus_faecalis, Enterococcus_faecium, Escherichia, Klebsiella_oxytoca, Klebsiella_pneumoniae, Neisseria_gonorrhoeae, Neisseria_meningitidis, Pseudomonas_aeruginosa, Salmonella, Serratia_marcescens, Staphylococcus_aureus, Staphylococcus_pseudintermedius, Streptococcus_agalactiae, Streptococcus_pneumoniae, Streptococcus_pyogenes, Vibrio_cholerae, Vibrio_parahaemolyticus, Vibrio_vulnificus

Burkholderia mallei is not specified in the list, nor as an option when I specify --list_organisms. Is my interpretation of the table incorrect or is there a mistake in the Documentation?

Thanks, Daniel

Danderson123 commented 1 week ago

Here is another one that is in the table but not valid when specifying--organism: Corynebacterium_diphtheriae. Is there a different organism option that would be suitable for these? Or is it best not to specify the species at all?

vbrover commented 1 week ago

The result of amrfinder --list_organisms is always correct. Please take a look at the version of amrfinder.

$ amrfinder --list_organisms
Running: ./amrfinder --list_organisms
Software directory: '/home/brovervv/work/amr/'
Software version: 3.12.8
Database directory: '/home/brovervv/work/amr/data/2024-07-22.1'
Database version: 2024-07-22.1

Available --organism options: Acinetobacter_baumannii, Burkholderia_cepacia, Burkholderia_mallei, Burkholderia_pseudomallei, Campylobacter, Citrobacter_freundii, Clostridioides_difficile, Corynebacterium_diphtheriae, Enterobacter_asburiae, Enterobacter_cloacae, Enterococcus_faecalis, Enterococcus_faecium, Escherichia, Klebsiella_oxytoca, Klebsiella_pneumoniae, Neisseria_gonorrhoeae, Neisseria_meningitidis, Pseudomonas_aeruginosa, Salmonella, Serratia_marcescens, Staphylococcus_aureus, Staphylococcus_pseudintermedius, Streptococcus_agalactiae, Streptococcus_pneumoniae, Streptococcus_pyogenes, Vibrio_cholerae, Vibrio_parahaemolyticus, Vibrio_vulnificus
Danderson123 commented 1 week ago

Ah I see, I am running the same version of amrfinder but a different database version:

Running: amrfinder --list_organisms
Software directory: '/homes/dander/software/bin/'
Software version: 3.12.8
Database directory: '/homes/dander/software/bin/data/2024-01-31.1'
Database version: 2024-01-31.1

Available --organism options: Acinetobacter_baumannii, Burkholderia_cepacia, Burkholderia_pseudomallei, Campylobacter, Citrobacter_freundii, Clostridioides_difficile, Enterobacter_asburiae, Enterobacter_cloacae, Enterococcus_faecalis, Enterococcus_faecium, Escherichia, Klebsiella_oxytoca, Klebsiella_pneumoniae, Neisseria_gonorrhoeae, Neisseria_meningitidis, Pseudomonas_aeruginosa, Salmonella, Serratia_marcescens, Staphylococcus_aureus, Staphylococcus_pseudintermedius, Streptococcus_agalactiae, Streptococcus_pneumoniae, Streptococcus_pyogenes, Vibrio_cholerae, Vibrio_parahaemolyticus, Vibrio_vulnificus

I have the results for most of my samples so I do not want to rerun using the latest database at this time. Would it be best to not specify the organism at all in that case?

vbrover commented 1 week ago

I have the results for most of my samples so I do not want to rerun using the latest database at this time.

amrfinder takes seconds, and I would rerun it on all samples using a parallel mechanism.

Would it be best to not specify the organism at all in that case?

This is possible. But then point mutations will not be reported. You can take a look at the file changes.txt where the database changes are listed.

Danderson123 commented 1 week ago

Ok, thanks for your help. Closing this now.

evolarjun commented 1 week ago

{quote} Would it be best to not specify the organism at all in that case? {quote} Yes, if you want to use the older version of the database just don't include the --organism option and it should run fine (just without the new organism specific point mutations).

I will try to clarify the help text that the available organisms depend on the database version as we add new organisms.