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
InputDownload latest card databasewget https://card.mcmaster.ca/download/0/broadstreet-v3.2.4.tar.bz2unzip into json filetar -xvf broadstreet-v3.2.4.tar.bz2 /myfolder/card.jsonload card database from jsondocker run --rm -it -v /myfolder:/card/ finlaymaguire/rgi bash -c "rgi load --card_json /card/card.json"run card annotationdocker 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
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.
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 filetar -xvf broadstreet-v3.2.4.tar.bz2 /myfolder/card.json
load card database from jsondocker run --rm -it -v /myfolder:/card/ finlaymaguire/rgi bash -c "rgi load --card_json /card/card.json"
run card annotationdocker 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 fileload 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.