The default value of minimum percent identity can be changed in the assign_taxonomy.py script under the __init__ method of the BlastTaxonAssigner class.

class BlastTaxonAssigner(TaxonAssigner):
    """ Assign taxon best on best blast hit above a threshold
    """
    Name = 'BlastTaxonAssigner'
    SeqsPerBlastRun = 1000
    def __init__(self, params):
        """ Initialize the object
        """
        _params = {
            'Min percent identity': 90.0,   # <<<< HERE
            'Max E value': 1e-30,
            'Application': 'blastn/megablast'
            }
        _params.update(params)
        TaxonAssigner.__init__(self, _params)

Hello, I have the same problem. I changed the parameter as mentioned above (I tried 97.0 and 99.0), but I still have the same results (i.e. if I blast a bad sequence manually, I get a %ID of 94 (for a 100% coverage), but the sequence is still assigned in my tax_assignment file. Did I miss something? Best, Noam

class BlastTaxonAssigner(TaxonAssigner):

""" Assign taxon best on best blast hit above a threshold
"""
Name = 'BlastTaxonAssigner'
SeqsPerBlastRun = 1000

def __init__(self, params):
    """ Initialize the object
    """
    _params = {
        'Min percent identity': 97.0,
        'Max E value': 1e-30,
        'Application': 'blastn/megablast'
    }