How to use the gtdbtk.exceptions.GTDBTkException function in gtdbtk

class GTDBTkExit(Exception):
    """Raised when GTDB-Tk is to quietly exit."""

    def __init__(self, message=''):
        Exception.__init__(self, message)


class GenomeNameInvalid(GTDBTkException):
    """ Thrown when a genome name contains characters which are not supported. """

    def __init__(self, message=''):
        GTDBTkException.__init__(self, message)


class GenomeBatchfileMalformed(GTDBTkException):
    """ Thrown when the format of the genome batchfile is malformed. """

    def __init__(self, message=''):
        GTDBTkException.__init__(self, message)


class NoGenomesFound(GTDBTkException):
    """ Thrown when no input genomes are found in a directory. """

    def __init__(self, message=''):
        GTDBTkException.__init__(self, message)


class ReferenceFileMalformed(GTDBTkException):
    """ Thrown when a reference file is malformed. """

class ProdigalException(GTDBTkException):
    """ Thrown when Prodigal returns a non-zero exit code. """

    def __init__(self, message=''):
        GTDBTkException.__init__(self, message)


class MSAMarkerLengthMismatch(GTDBTkException):
    """ Thrown when an MSA length does not equal the length of the markers. """

    def __init__(self, message=''):
        GTDBTkException.__init__(self, message)


class MSAMaskLengthMismatch(GTDBTkException):
    """ Thrown when an MSA length does not equal the length of the mask. """

    def __init__(self, message=''):
        GTDBTkException.__init__(self, message)


class PplacerException(GTDBTkException):
    """ Thrown whenever an error is encountered while running pplacer. """

    def __init__(self, message=''):
        GTDBTkException.__init__(self, message)


class TogException(GTDBTkException):
    """ Thrown whenever an error is encountered while running tog. """

def __init__(self, message=''):
        GTDBTkException.__init__(self, message)

class MSAMaskLengthMismatch(GTDBTkException):
    """ Thrown when an MSA length does not equal the length of the mask. """

    def __init__(self, message=''):
        GTDBTkException.__init__(self, message)


class PplacerException(GTDBTkException):
    """ Thrown whenever an error is encountered while running pplacer. """

    def __init__(self, message=''):
        GTDBTkException.__init__(self, message)


class TogException(GTDBTkException):
    """ Thrown whenever an error is encountered while running tog. """

    def __init__(self, message=''):
        GTDBTkException.__init__(self, message)


class FastANIException(GTDBTkException):
    """ Thrown when an exception is encountered while running FastANI. """

    def __init__(self, message=''):
        GTDBTkException.__init__(self, message)


class FastTreeException(GTDBTkException):
    """ Thrown when an exception is encountered while running FastTree. """

class ReferenceFileMalformed(GTDBTkException):
    """ Thrown when a reference file is malformed. """

    def __init__(self, message=''):
        GTDBTkException.__init__(self, message)


class GenomeMarkerSetUnknown(GTDBTkException):
    """ Thrown when the genome marker set is unknown (i.e. not ar122, or bac120). """

    def __init__(self, message=''):
        GTDBTkException.__init__(self, message)


class InconsistentGenomeBatch(GTDBTkException):
    """ Thrown when number of genomes in the identify directory is different than the number of genomes to process. """

    def __init__(self, message=''):
        GTDBTkException.__init__(self, message)


class FileNotFound(GTDBTkException):
    """ Thrown when a file is not found. """

    def __init__(self, message=''):
        GTDBTkException.__init__(self, message)


class DirNotFound(GTDBTkException):
    """ Thrown when a directory is not found. """

class NoGenomesFound(GTDBTkException):
    """ Thrown when no input genomes are found in a directory. """

    def __init__(self, message=''):
        GTDBTkException.__init__(self, message)


class ReferenceFileMalformed(GTDBTkException):
    """ Thrown when a reference file is malformed. """

    def __init__(self, message=''):
        GTDBTkException.__init__(self, message)


class GenomeMarkerSetUnknown(GTDBTkException):
    """ Thrown when the genome marker set is unknown (i.e. not ar122, or bac120). """

    def __init__(self, message=''):
        GTDBTkException.__init__(self, message)


class InconsistentGenomeBatch(GTDBTkException):
    """ Thrown when number of genomes in the identify directory is different than the number of genomes to process. """

    def __init__(self, message=''):
        GTDBTkException.__init__(self, message)


class FileNotFound(GTDBTkException):
    """ Thrown when a file is not found. """

class GenomeMarkerSetUnknown(GTDBTkException):
    """ Thrown when the genome marker set is unknown (i.e. not ar122, or bac120). """

    def __init__(self, message=''):
        GTDBTkException.__init__(self, message)


class InconsistentGenomeBatch(GTDBTkException):
    """ Thrown when number of genomes in the identify directory is different than the number of genomes to process. """

    def __init__(self, message=''):
        GTDBTkException.__init__(self, message)


class FileNotFound(GTDBTkException):
    """ Thrown when a file is not found. """

    def __init__(self, message=''):
        GTDBTkException.__init__(self, message)


class DirNotFound(GTDBTkException):
    """ Thrown when a directory is not found. """

    def __init__(self, message=''):
        GTDBTkException.__init__(self, message)


class ProdigalException(GTDBTkException):
    """ Thrown when Prodigal returns a non-zero exit code. """

class GenomeNameInvalid(GTDBTkException):
    """ Thrown when a genome name contains characters which are not supported. """

    def __init__(self, message=''):
        GTDBTkException.__init__(self, message)


class GenomeBatchfileMalformed(GTDBTkException):
    """ Thrown when the format of the genome batchfile is malformed. """

    def __init__(self, message=''):
        GTDBTkException.__init__(self, message)


class NoGenomesFound(GTDBTkException):
    """ Thrown when no input genomes are found in a directory. """

    def __init__(self, message=''):
        GTDBTkException.__init__(self, message)


class ReferenceFileMalformed(GTDBTkException):
    """ Thrown when a reference file is malformed. """

    def __init__(self, message=''):
        GTDBTkException.__init__(self, message)


class GenomeMarkerSetUnknown(GTDBTkException):
    """ Thrown when the genome marker set is unknown (i.e. not ar122, or bac120). """

class FileNotFound(GTDBTkException):
    """ Thrown when a file is not found. """

    def __init__(self, message=''):
        GTDBTkException.__init__(self, message)


class DirNotFound(GTDBTkException):
    """ Thrown when a directory is not found. """

    def __init__(self, message=''):
        GTDBTkException.__init__(self, message)


class ProdigalException(GTDBTkException):
    """ Thrown when Prodigal returns a non-zero exit code. """

    def __init__(self, message=''):
        GTDBTkException.__init__(self, message)


class MSAMarkerLengthMismatch(GTDBTkException):
    """ Thrown when an MSA length does not equal the length of the markers. """

    def __init__(self, message=''):
        GTDBTkException.__init__(self, message)


class MSAMaskLengthMismatch(GTDBTkException):
    """ Thrown when an MSA length does not equal the length of the mask. """

:param path: Path to the genomic fasta file for the genome
        :param marker_set_id: Unique ID of marker set to use for alignment
        """

        cur_marker_dir = os.path.dirname(os.path.dirname(path))
        pfam_tophit_file = TopHitPfamFile(cur_marker_dir, db_genome_id)
        tigr_tophit_file = TopHitTigrFile(cur_marker_dir, db_genome_id)
        pfam_tophit_file.read()
        tigr_tophit_file.read()

        if marker_set_id == 'bac120':
            copy_number_file = CopyNumberFileBAC120('/dev/null', None)
        elif marker_set_id == 'ar122':
            copy_number_file = CopyNumberFileAR122('/dev/null', None)
        else:
            raise GTDBTkException('Unknown marker set.')

        copy_number_file.add_genome(db_genome_id, path, pfam_tophit_file, tigr_tophit_file)
        single_copy_hits = copy_number_file.get_single_copy_hits(db_genome_id)

        # gather information for all marker genes
        marker_paths = {"PFAM": os.path.join(self.pfam_hmm_dir, 'individual_hmms'),
                        "TIGRFAM": os.path.join(os.path.dirname(self.tigrfam_hmm_dir), 'individual_hmms')}

        marker_dict_original = {}
        if marker_set_id == "bac120":
            for db_marker in sorted(self.bac120_markers):
                marker_dict_original.update({marker.replace(".HMM", "").replace(".hmm", ""):
                                             os.path.join(
                    marker_paths[db_marker], marker)
                    for marker in self.bac120_markers[db_marker]})
        elif marker_set_id == "ar122":