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 copy json file when loading CARD Reference Data #193

Closed BangzhuoTong closed 10 months ago

BangzhuoTong commented 2 years ago

Describe the bug fail to run rgi card_annotation

Input Download latest card database wget https://card.mcmaster.ca/download/0/broadstreet-v3.2.4.tar.bz2 unzip into json file tar -xvf broadstreet-v3.2.4.tar.bz2 /myfolder/card.json load card database from json docker run --rm -it -v /myfolder:/card/ finlaymaguire/rgi bash -c "rgi load --card_json /card/card.json" run card annotation docker run --rm -it -v /myfolder:/card/ finlaymaguire/rgi bash -c "rgi card_annotation -i /card/card.json > /card/card_annotation.log" Something already went wrong above because noting was written to card_annotation.log file
load annotated card database, version should be 3.2.4, which is the same as the version of downloaded card database.
docker run --rm -it -v /myfolder:/card/ finlaymaguire/rgi bash -c "rgi load -i /card/card.json --card_annotation card_database_v3.2.4.fasta --local" Error occur in last step: failed to copy json file: [Errno 2] No such file or directory: 'card_database_v3.2.4.fasta'

Input file The file you used as an input to run the data. Either paste a sample or upload the file.

Error log failed to copy json file: [Errno 2] No such file or directory: 'card_database_v3.2.4.fasta'

CARD Version 3.2.4

RGI version lastest docker image. finlaymaguire/rgi:latest

Expected behavior load annotated card_database_v3.2.4.fasta

Screenshots If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information): Linux server x86_64 GNU/Linux

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

lpbbbbbb commented 1 year ago

Hellow sir, I met the same problem. can you give me some adadvice vice to solve this?

github-actions[bot] commented 10 months ago

Issue is stale and will be closed in 7 days unless there is new activity