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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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[BUG] Error locating paths / singularity #215

Closed camilagazolla closed 10 months ago

camilagazolla commented 1 year ago

Hello,

I am struggling to create the CARD annotation files. Any idea of what may be the cause of this error?

Apparently, RGI is not properly locating the paths given.

Input

  1. Trying to create the CARD annotation files

    wget https://card.mcmaster.ca/latest/data
tar -xvf data ./card.json
singularity run -c rgi_5.1.1--py_0.sif rgi card_annotation -i /home/cgazollavolpiano/card.json > card_annotation.log 2>&1

  2. Trying to locate an input file

    singularity run -c rgi_5.1.1--py_0.sif rgi main --input_sequence test/nucleotide_input.fasta --output_file test/output_file --local --clean

    The path for card.json and nucleotide_input.fasta are both right...

Error log Screenshot 2023-02-02 at 3 27 34 pm

Screenshot 2023-02-02 at 3 46 10 pm

RGI version Resistance Gene Identifier - 5.1.1

Desktop:

Additional context RGI installed using singularity. Maybe the "WARNING: Skipping mount /var/lib/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container" is related to the problem? The conda installation options is not working (stuck at solving environment)

Thank you in advance! :)

github-actions[bot] commented 10 months ago

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