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phac-nml / staramr

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
Apache License 2.0
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cant run staramr #181

Closed Hedi65 closed 1 year ago

Hedi65 commented 1 year ago

dear community

im trying to run staramr but for some reason staramr give me an error saying my fasta file does not exist.

here is my command line: staramr search -o test myfile.fasta

I'm sure no misspelling occurred while typing the path and file name.

thanks for your input

apetkau commented 1 year ago

What does myfile.fasta look like? Is it possible there's spaces or other invisible characters in the file name? Is the command being run on a local machine or being submitted to a computational cluster (where it's possible different cluster nodes could see different files)?

Unfortunately, I do not have too many ideas on what the issue could be.

apetkau commented 1 year ago

Another possibility, if you are running in a container like Docker, is that the file does not exist within the container. In this case, you may need to mount the current directory as a volume and use full paths. For example:

docker run -v $PWD:$PWD staramr-image:latest staramr -o $PWD/test $PWD/myflie.fasta

($PWD contains the current working directory).

apetkau commented 1 year ago

Closing this issue. If it is has still remained unresolved feel free to re-open.