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arpcard / rgi

Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.
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failed to load latest card database(version 3.2.8) using docker rgi(latest) #252

Closed hemantgoyat22 closed 6 months ago

hemantgoyat22 commented 9 months ago

Describe the bug fail to load latest card database(version 3.2.8) using docker rgi(latest).

Input Download latest card database wget https://card.mcmaster.ca/latest/data unzip into json file tar -xvf data /Path/to/card-data.tar.bz2 load card database from json docker run -v $PWD:/data finlaymaguire/rgi rgi load --card_json /Path/to/card.json

Input file Unzipped card.json file.

Error log ERROR conda.cli.main_run:execute(41): conda run rgi load --card_json /Users/hemantgoyat/Downloads/card-data/card.json failed. (See above for error). FileNotFoundError: [Errno 2] No such file or directory: '/Users/hemantgoyat/Downloads/card-data/card.json'

CARD Version Currently loaded version is 3.2.5. Desired version that i want to load is 3.2.8

RGI version Latest RGI version. docker pull finlaymaguire/rgi:latest

Expected behavior load latest card database (version3.2.8), (file name = card.json)

Screenshots

Card_database_load_error

Desktop (please complete the following information):

Additional context Add any other context about the problem here. If applicable, include dependency versions such as Biopython version and Python version.

raphenya commented 6 months ago

@hemantgoyat22 see https://github.com/arpcard/rgi/issues/144