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WatsonLab / PULpy

Open prediction of Polysaccharide Utilisation Loci (PUL)
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Error in rule proteins #6

Open BenedicteColnet opened 4 years ago

BenedicteColnet commented 4 years ago

Hi!

Trying to run your tool I have an error message saying:

Error in rule proteins:
    jobid: 6
    output: proteins/test_protein.faa, proteins/test_prodigal.gff
    conda-env: /PULpy/.snakemake/conda/3a6f6077
    shell:
        zcat genomes/test_genomic.fna.gz | prodigal -a proteins/test_protein.faa -q -f gff > proteins/test_prodigal.gff
        (exited with non-zero exit code)

Prodigal is well installed and when running a similar line that the one mentioned in your code it works.

Thank you by advance for your answer!

mw55309 commented 4 years ago

Is zcat installed on your system?