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CMD Issue with diamond 2.0.5 & funannotate-p2g #529

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casett opened this issue Jan 11, 2021 · 1 comment
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CMD Issue with diamond 2.0.5 & funannotate-p2g #529

casett opened this issue Jan 11, 2021 · 1 comment

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@casett
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casett commented Jan 11, 2021

I am getting a CMD error when using diamond 2.0.5 with funannotate predict (using v. 1.8.3). I believe there is a small coding error on line 97 and that '-c1' should be '-c', '1' in https://github.com/nextgenusfs/funannotate/blob/master/funannotate/aux_scripts/funannotate-p2g.py

Here is the chunk of code I am referring to:

def runDiamond(input, query, cpus, output, premade_db=None):
    # create DB of protein sequences
    # check diamond version
    if lib.getDiamondVersion() >= '2.0.5':
        # run in frameshift mode
        cmd = ['diamond', 'blastx', '--threads', str(cpus), '-q', input,
               '--db', 'diamond', '-o', 'diamond.matches.tab', '-e', '1e-10',
               '-k', '0', '--more-sensitive', '--unal', '0', '-c1', '-F', '15',
               '-f', '6', 'sseqid', 'slen',
               'sstart', 'send', 'qseqid', 'qlen', 'qstart', 'qend', 'pident',
               'length', 'evalue', 'score', 'qcovhsp', 'qframe']

nextgenusfs pushed a commit that referenced this issue Jan 11, 2021
@nextgenusfs
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Pushed the fix, I don't see this error in the docker container that's running v2.0.6.

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