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amrfinder running with options --ident_min and --coverage_min #126

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stalact opened this issue Jun 20, 2023 · 2 comments
Closed

amrfinder running with options --ident_min and --coverage_min #126

stalact opened this issue Jun 20, 2023 · 2 comments
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bug Something isn't working can't reproduce Bug or apparent bug that we can't yet reproduce

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@stalact
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stalact commented Jun 20, 2023

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
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vbrover commented Jun 20, 2023

Could you post genome.fna?

@evolarjun evolarjun added the bug Something isn't working label Jun 21, 2023
@evolarjun evolarjun added the can't reproduce Bug or apparent bug that we can't yet reproduce label Sep 13, 2023
@evolarjun
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Resolving since we don't have test data. Please reopen and include test data if this is still an issue.

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Labels
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