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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
'-c1'
'-c', '1'
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']
The text was updated successfully, but these errors were encountered:
fix for #529
dc0e497
Pushed the fix, I don't see this error in the docker container that's running v2.0.6.
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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.pyHere is the chunk of code I am referring to:
The text was updated successfully, but these errors were encountered: