def main():
# -------------------------------------------------
# get and check options
args = None
if len(sys.argv) == 1:
print_help()
sys.exit(0)
elif sys.argv[1] in {'-v', '--v', '-version', '--version'}:
print(f"gtdbtk: version {__version__} {__copyright__} {__author__}")
# Warn the user they are not using the latest version (if possible)
latest_ver = get_gtdbtk_latest_version()
if latest_ver and latest_ver != __version__:
print(f'Note: There is a newer version of GTDB-Tk available: v{latest_ver}')
sys.exit(0)
elif sys.argv[1] in {'-h', '--h', '-help', '--help'}:
print_help()
sys.exit(0)
else:
args = get_main_parser().parse_args()
# setup logger
logger_setup(args.out_dir if hasattr(args, 'out_dir') else None,
"gtdbtk.log", "GTDB-Tk", __version__, False,
hasattr(args, 'debug') and args.debug)
logger = logging.getLogger('timestamp')
# -------------------------------------------------
# do what we came here to do
try:
gt_parser = OptionsParser(__version__)
gt_parser.parse_options(args)
except SystemExit:
logger.error('Controlled exit resulting from early termination.')
sys.exit(1)
except KeyboardInterrupt:
logger.error('Controlled exit resulting from interrupt signal.')
sys.exit(1)
except GTDBTkExit as e:
if len(str(e)) > 0:
logger.error('{}'.format(e))
logger.error('Controlled exit resulting from an unrecoverable error or warning.')
sys.exit(1)
except (GTDBTkException, BioLibError) as e:
msg = 'Controlled exit resulting from an unrecoverable error or warning.\n\n'
msg += '=' * 80 + '\n'
msg += 'EXCEPTION: {}\n'.format(type(e).__name__)
msg += ' MESSAGE: {}\n'.format(e)
msg += '_' * 80 + '\n\n'
msg += traceback.format_exc()
msg += '=' * 80
logger.error(msg)
sys.exit(1)
except Exception as e:
msg = 'Uncontrolled exit resulting from an unexpected error.\n\n'
msg += '=' * 80 + '\n'
msg += 'EXCEPTION: {}\n'.format(type(e).__name__)
msg += ' MESSAGE: {}\n'.format(e)
msg += '_' * 80 + '\n\n'
msg += traceback.format_exc()
msg += '=' * 80
logger.error(msg)
sys.exit(1)
def main():
parser = argparse.ArgumentParser(prog='gtdbtk',
add_help=False,
conflict_handler='resolve')
parser.add_argument('-f',
'--force',
action="store_true",
default=False,
help="overwrite existing files without prompting.")
subparsers = parser.add_subparsers(help="--", dest='subparser_name')
# de novo workflow
denovo_wf_parser = subparsers.add_parser(
'de_novo_wf',
conflict_handler='resolve',
formatter_class=CustomHelpFormatter,
help='Infer de novo tree and decorate with GTDB taxonomy.')
mutual_genome_denovo_wf = denovo_wf_parser.add_argument_group(
'mutually exclusive required arguments')
mutex_group = mutual_genome_denovo_wf.add_mutually_exclusive_group(
required=True)
mutex_group.add_argument(
'--genome_dir',
help="directory containing genome files in FASTA format")
mutex_group.add_argument(
'--batchfile',
help=
"file describing genomes - tab separated in 2 columns (FASTA file, genome ID)"
)
mutual_ms_denovo_wf = denovo_wf_parser.add_argument_group(
'mutually exclusive required arguments')
mutex_group = mutual_ms_denovo_wf.add_mutually_exclusive_group(
required=True)
mutex_group.add_argument('--bacteria',
action='store_true',
help='process bacterial genomes')
mutex_group.add_argument('--archaea',
action='store_true',
help='process archaeal genomes')
required_denovo_wf = denovo_wf_parser.add_argument_group(
'required named arguments')
required_denovo_wf.add_argument(
'--outgroup_taxon',
required=True,
help=
"taxon to use as outgroup (e.g., p__Patescibacteria or p__Altiarchaeota)"
)
required_denovo_wf.add_argument('--out_dir',
required=True,
help="directory to output files")
optional_denovo_wf = denovo_wf_parser.add_argument_group(
'optional arguments')
optional_denovo_wf.add_argument(
'-x',
'--extension',
default='fna',
help='extension of files to process, gz = gzipped')
optional_denovo_wf.add_argument(
'--skip_gtdb_refs',
action="store_true",
help=
'do not include GTDB reference genomes in multiple sequence alignment')
optional_denovo_wf.add_argument(
'--taxa_filter',
help=('filter GTDB genomes to taxa (comma separated) within ' +
'specific taxonomic groups (e.g., d__Bacteria ' +
'or p__Proteobacteria, p__Actinobacteria)'))
optional_denovo_wf.add_argument(
'--min_perc_aa',
type=float,
default=10,
help=
'filter genomes with an insufficient percentage of AA in the MSA (inclusive bound)'
)
optional_denovo_wf.add_argument(
'--custom_msa_filters',
action="store_true",
help=
('perform custom filtering of MSA with cols_per_gene, min_consensus ' +
'max_consensus, and min_perc_taxa parameters instead of using canonical mask'
))
optional_denovo_wf.add_argument(
'--cols_per_gene',
type=int,
default=42,
help='maximum number of columns to retain per gene')
optional_denovo_wf.add_argument(
'--min_consensus',
type=float,
default=25,
help=
'minimum percentage of the same amino acid required to retain column (inclusive bound)'
)
optional_denovo_wf.add_argument(
'--max_consensus',
type=float,
default=95,
help=
'maximum percentage of the same amino acid required to retain column (exclusive bound)'
)
optional_denovo_wf.add_argument(
'--min_perc_taxa',
type=float,
default=50,
help=
'minimum percentage of taxa required to retain column (inclusive bound)'
)
optional_denovo_wf.add_argument(
'--rnd_seed',
type=int,
default=None,
help='random seed to use for selecting columns')
optional_denovo_wf.add_argument(
'--prot_model',
choices=['JTT', 'WAG', 'LG'],
help='protein substitution model for tree inference',
default='WAG')
optional_denovo_wf.add_argument(
'--no_support',
action="store_true",
help=
"do not compute local support values using the Shimodaira-Hasegawa test"
)
optional_denovo_wf.add_argument(
'--gamma',
action="store_true",
help="rescale branch lengths to optimize the Gamma20 likelihood")
optional_denovo_wf.add_argument(
'--gtdbtk_classification_file',
help=
"file with GTDB-Tk classifications produced by the `classify` command")
optional_denovo_wf.add_argument(
'--custom_taxonomy_file',
help=
"file indicating custom taxonomy string for at least the genomes belonging to the outgroup"
)
optional_denovo_wf.add_argument('--prefix',
default='gtdbtk',
help='desired prefix for output files')
optional_denovo_wf.add_argument('--cpus',
default=1,
type=int,
help='number of CPUs to use')
optional_denovo_wf.add_argument(
'--force',
action='store_const',
const=True,
default=False,
help='continue processing if an error occurs on a single genome')
optional_denovo_wf.add_argument(
'--debug',
action="store_true",
help='create intermediate files for debugging purposes')
optional_denovo_wf.add_argument('-h',
'--help',
action="help",
help="show help message")
# classify workflow
classify_wf_parser = subparsers.add_parser(
'classify_wf',
conflict_handler='resolve',
formatter_class=CustomHelpFormatter,
help='Classify genomes by placement in GTDB reference tree.')
mutual_genome_classify_wf = classify_wf_parser.add_argument_group(
'mutually exclusive required arguments')
mutex_group = mutual_genome_classify_wf.add_mutually_exclusive_group(
required=True)
mutex_group.add_argument(
'--genome_dir',
help="directory containing genome files in FASTA format")
mutex_group.add_argument(
'--batchfile',
help=
"file describing genomes - tab separated in 3 columns (FASTA file, genome ID, translation table [optional])"
)
required_classify_wf = classify_wf_parser.add_argument_group(
'required named arguments')
required_classify_wf.add_argument('--out_dir',
required=True,
help="directory to output files")
optional_classify_wf = classify_wf_parser.add_argument_group(
'optional arguments')
optional_classify_wf.add_argument(
'-x',
'--extension',
default='fna',
help='extension of files to process, gz = gzipped')
optional_classify_wf.add_argument(
'--min_perc_aa',
type=float,
default=10,
help='filter genomes with an insufficient percentage of AA in the MSA')
optional_classify_wf.add_argument('--prefix',
required=False,
default='gtdbtk',
help='desired prefix for output files')
optional_classify_wf.add_argument('--cpus',
default=1,
type=int,
help='number of CPUs to use')
optional_classify_wf.add_argument(
'--pplacer_cpus',
type=int,
default=None,
help='use PPLACER_CPUS during placement (default: CPUS)')
optional_classify_wf.add_argument(
'--force',
action='store_const',
const=True,
default=False,
help='continue processing if an error occurs on a single genome')
optional_classify_wf.add_argument(
'--scratch_dir',
help='Reduce memory usage by writing to disk (slower).')
optional_classify_wf.add_argument(
'-r',
'--recalculate_red',
action='store_true',
help=
'recalculate RED values based on the reference tree and all added user genomes'
)
# optional_classify_wf.add_argument('-s', '--split_tree', action='store_true',
# help='Use shards of the reference tree (for Bacteria only). reduce memory usage (slower).')
optional_classify_wf.add_argument(
'-d',
'--debug',
action="store_true",
help='create intermediate files for debugging purposes')
optional_classify_wf.add_argument('-h',
'--help',
action="help",
help="show help message")
# identify marker genes in genomes
identify_parser = subparsers.add_parser(
'identify',
conflict_handler='resolve',
formatter_class=CustomHelpFormatter,
help='Identify marker genes in genome.')
mutex_identify = identify_parser.add_argument_group(
'mutually exclusive required arguments')
mutex_group = mutex_identify.add_mutually_exclusive_group(required=True)
mutex_group.add_argument(
'--genome_dir',
help="directory containing genome files in FASTA format")
mutex_group.add_argument(
'--batchfile',
help=
"file describing genomes - tab separated in 3 columns (FASTA file, genome ID, translation table [optional])"
)
required_identify = identify_parser.add_argument_group(
'required named arguments')
required_identify.add_argument('--out_dir',
required=True,
help="directory to output files")
optional_identify = identify_parser.add_argument_group(
'optional arguments')
optional_identify.add_argument(
'-x',
'--extension',
default='fna',
help='extension of files to process, gz = gzipped')
optional_identify.add_argument('--prefix',
default='gtdbtk',
help='desired prefix for output files')
optional_identify.add_argument('--cpus',
default=1,
type=int,
help='number of CPUs to use')
optional_identify.add_argument(
'--force',
action='store_const',
const=True,
default=False,
help='continue processing if an error occurs on a single genome')
optional_identify.add_argument('-h',
'--help',
action="help",
help="show help message")
# create multiple sequence alignment
align_parser = subparsers.add_parser(
'align',
conflict_handler='resolve',
formatter_class=CustomHelpFormatter,
help='Create multiple sequence alignment.',
)
required_align = align_parser.add_argument_group(
'required named arguments')
required_align.add_argument('--identify_dir',
required=True,
help="output directory of 'identify' command")
required_align.add_argument('--out_dir',
required=True,
help='directory to output files')
optional_align = align_parser.add_argument_group('optional arguments')
optional_align.add_argument(
'--skip_gtdb_refs',
action="store_true",
help=
'do not include GTDB reference genomes in multiple sequence alignment')
optional_align.add_argument(
'--taxa_filter',
help=('filter GTDB genomes to taxa (comma separated) within ' +
'specific taxonomic groups (e.g., d__Bacteria ' +
'or p__Proteobacteria, p__Actinobacteria)'))
optional_align.add_argument(
'--min_perc_aa',
type=float,
default=10,
help=
'filter genomes with an insufficient percentage of AA in the MSA (inclusive bound)'
)
mutual_genome_align = align_parser.add_argument_group(
'mutually exclusive optional arguments')
mutex_align_group = mutual_genome_align.add_mutually_exclusive_group()
mutex_align_group.add_argument(
'--custom_msa_filters',
action="store_true",
help=
('perform custom filtering of MSA with cols_per_gene, min_consensus ' +
'max_consensus, and min_perc_taxa parameters instead of using canonical mask'
))
mutex_align_group.add_argument(
'--skip_trimming',
action="store_true",
default=False,
help='skip trimming step and return the full MSAs')
optional_align.add_argument(
'--cols_per_gene',
type=int,
default=42,
help='maximum number of columns to retain per gene')
optional_align.add_argument(
'--min_consensus',
type=float,
default=25,
help=
'minimum percentage of the same amino acid required to retain column (inclusive bound)'
)
optional_align.add_argument(
'--max_consensus',
type=float,
default=95,
help=
'maximum percentage of the same amino acid required to retain column (exclusive bound)'
)
optional_align.add_argument(
'--min_perc_taxa',
type=float,
default=50,
help=
'minimum percentage of taxa required to retain column (inclusive bound)'
)
optional_align.add_argument(
'--rnd_seed',
type=int,
default=None,
help='random seed to use for selecting columns')
optional_align.add_argument('--prefix',
required=False,
default='gtdbtk',
help='desired prefix for output files')
optional_align.add_argument('--cpus',
default=1,
type=int,
help='number of CPUs to use')
optional_align.add_argument(
'--debug',
action="store_true",
help='create intermediate files for debugging purposes')
optional_align.add_argument('-h',
'--help',
action="help",
help="show help message")
# infer tree
infer_parser = subparsers.add_parser(
'infer',
conflict_handler='resolve',
formatter_class=CustomHelpFormatter,
help='Infer tree from multiple sequence alignment.',
)
required_infer = infer_parser.add_argument_group(
'required named arguments')
required_infer.add_argument(
'--msa_file',
required=True,
help="multiple sequence alignment in FASTA format")
required_infer.add_argument('--out_dir',
required=True,
help='directory to output files')
optional_infer = infer_parser.add_argument_group('optional arguments')
optional_infer.add_argument(
'--prot_model',
choices=['JTT', 'WAG', 'LG'],
help='protein substitution model for tree inference',
default='WAG')
optional_infer.add_argument(
'--no_support',
action="store_true",
help=
"do not compute local support values using the Shimodaira-Hasegawa test"
)
optional_infer.add_argument(
'--gamma',
action="store_true",
help="rescale branch lengths to optimize the Gamma20 likelihood")
optional_infer.add_argument('--prefix',
required=False,
default='gtdbtk',
help='desired prefix for output files')
optional_infer.add_argument('--cpus',
default=1,
type=int,
help='number of CPUs to use')
optional_infer.add_argument('-h',
'--help',
action="help",
help="show help message")
# classify genomes via placement with pplacer
classify_parser = subparsers.add_parser(
'classify',
conflict_handler='resolve',
formatter_class=CustomHelpFormatter,
help='Determine taxonomic classification of genomes.',
)
mutual_genome_classify = classify_parser.add_argument_group(
'mutually exclusive required arguments')
mutex_group = mutual_genome_classify.add_mutually_exclusive_group(
required=True)
mutex_group.add_argument(
'--genome_dir',
help="directory containing genome files in FASTA format")
mutex_group.add_argument(
'--batchfile',
help=
"file describing genomes - tab separated in 2 columns (FASTA file, genome ID)"
)
required_classify = classify_parser.add_argument_group(
'required named arguments')
required_classify.add_argument('--align_dir',
required=True,
help="output directory of 'align' command")
required_classify.add_argument('--out_dir',
required=True,
help='directory to output files')
optional_classify = classify_parser.add_argument_group(
'optional arguments')
optional_classify.add_argument(
'-x',
'--extension',
default='fna',
help='extension of files to process, gz = gzipped')
optional_classify.add_argument('--prefix',
required=False,
default='gtdbtk',
help='desired prefix for output files')
optional_classify.add_argument('--cpus',
default=1,
type=int,
help='number of CPUs to use')
optional_classify.add_argument(
'--pplacer_cpus',
type=int,
default=None,
help='use PPLACER_CPUS during placement (default: CPUS)')
optional_classify.add_argument(
'--scratch_dir',
help='reduce memory usage by writing to disk (slower)')
# optional_classify.add_argument('-s', '--split_tree', action='store_true',
# help='Use shards of the reference tree (for Bacteria only). reduce memory usage (slower).')
optional_classify.add_argument(
'-r',
'--recalculate_red',
action='store_true',
help=
'recalculate RED values based on the reference tree and all added user genomes'
)
optional_classify.add_argument(
'--debug',
action="store_true",
help='create intermediate files for debugging purposes')
optional_classify.add_argument('-h',
'--help',
action="help",
help="show help message")
# root tree using outgroup
root_parser = subparsers.add_parser(
'root',
conflict_handler='resolve',
formatter_class=CustomHelpFormatter,
help='Root tree using an outgroup.',
)
required_root = root_parser.add_argument_group('required named arguments')
required_root.add_argument('--input_tree',
required=True,
help="tree to root in Newick format")
required_root.add_argument(
'--outgroup_taxon',
required=True,
help=
"taxon to use as outgroup (e.g., p__Patescibacteria or p__Altiarchaeota)"
)
required_root.add_argument('--output_tree',
required=True,
help='output tree')
optional_root = root_parser.add_argument_group('optional arguments')
optional_root.add_argument(
'--gtdbtk_classification_file',
help=
"file with GTDB-Tk classifications produced by the `classify` command")
optional_root.add_argument(
'--custom_taxonomy_file',
help=
"file indicating custom taxonomy strings for user genomes, which should contain any genomes belonging to the outgroup"
)
optional_root.add_argument('-h',
'--help',
action="help",
help="show help message")
# decorate tree
decorate_parser = subparsers.add_parser(
'decorate',
conflict_handler='resolve',
formatter_class=CustomHelpFormatter,
help='Decorate tree with GTDB taxonomy.',
)
required_decorate = decorate_parser.add_argument_group(
'required named arguments')
required_decorate.add_argument('--input_tree',
required=True,
help="tree to root in Newick format")
required_decorate.add_argument('--output_tree',
required=True,
help='output tree')
optional_decorate = decorate_parser.add_argument_group(
'optional arguments')
optional_decorate.add_argument(
'--gtdbtk_classification_file',
help=
"file with GTDB-Tk classifications produced by the `classify` command")
optional_decorate.add_argument(
'--custom_taxonomy_file',
help="file indicating custom taxonomy strings for user genomes")
optional_decorate.add_argument('-h',
'--help',
action="help",
help="show help message")
# establish taxonomic ranks of internal nodes using RED
infer_ranks_parser = subparsers.add_parser(
'infer_ranks',
conflict_handler='resolve',
formatter_class=CustomHelpFormatter,
help='Establish taxonomic ranks of internal nodes using RED.',
)
infer_ranks_req = infer_ranks_parser.add_argument_group(
'required named arguments')
infer_ranks_req.add_argument(
'--input_tree',
required=True,
help="rooted input tree with labelled ingroup taxon")
infer_ranks_req.add_argument(
'--ingroup_taxon',
required=True,
help=
"labelled ingroup taxon to use as root for establish RED values (e.g., c__Bacilli or f__Lactobacillaceae"
)
infer_ranks_req.add_argument('--output_tree',
required=True,
help="output tree")
infer_ranks_opt = infer_ranks_parser.add_argument_group(
'optional arguments')
infer_ranks_opt.add_argument('-h',
'--help',
action="help",
help="show help message")
# ani_rep
ani_rep_parser = subparsers.add_parser(
'ani_rep',
conflict_handler='resolve',
formatter_class=CustomHelpFormatter,
help='Calculates ANI to GTDB representative genomes.',
)
# ani_rep mutex required input genomes
ani_rep_mutex_genome = ani_rep_parser.add_argument_group(
'mutually exclusive required arguments')
ani_rep_mutex_in = ani_rep_mutex_genome.add_mutually_exclusive_group(
required=True)
ani_rep_mutex_in.add_argument(
'--genome_dir',
help="directory containing genome files in FASTA format")
ani_rep_mutex_in.add_argument(
'--batchfile',
help=
"file describing genomes - tab separated in 2 columns (FASTA file, genome ID)"
)
# ani_rep required arguments
ani_rep_req = ani_rep_parser.add_argument_group('required named arguments')
ani_rep_req.add_argument('--out_dir',
required=True,
help="directory to output files")
# ani_rep mash arguments
ani_rep_mash = ani_rep_parser.add_argument_group('optional Mash arguments')
ani_rep_mash.add_argument('--no_mash',
action='store_const',
const=True,
default=False,
help='skip pre-filtering using MASH')
ani_rep_mash.add_argument('--mash_k',
default=16,
type=int,
help='k-mer size [1-32]')
ani_rep_mash.add_argument('--mash_s',
default=5000,
type=int,
help='maximum number of non-redundant hashes')
ani_rep_mash.add_argument('--mash_d',
default=0.1,
type=float,
help='maximum distance to keep [0-1]')
ani_rep_mash.add_argument('--mash_v',
default=1.0,
type=float,
help='maximum p-value to keep [0-1]')
ani_rep_fastani_opt = ani_rep_parser.add_argument_group(
'optional FastANI arguments')
ani_rep_fastani_opt.add_argument(
'--min_af',
default=AF_THRESHOLD,
type=float,
help='alignment fraction to consider closest genome')
# ani_rep optional arguments
ani_rep_opt = ani_rep_parser.add_argument_group('optional arguments')
ani_rep_opt.add_argument(
'-x',
'--extension',
default='fna',
help='extension of files to process, gz = gzipped')
ani_rep_opt.add_argument('--prefix',
default='gtdbtk',
help='desired prefix for output files')
ani_rep_opt.add_argument('--cpus',
default=1,
type=int,
help='number of CPUs to use')
ani_rep_opt.add_argument('-h',
'--help',
action="help",
help="show help message")
# test
test_parser = subparsers.add_parser(
'test',
conflict_handler='resolve',
formatter_class=CustomHelpFormatter,
help='Test the classify_wf pipeline with 3 archaeal genomes.')
required_test = test_parser.add_argument_group('required named arguments')
required_test.add_argument('--out_dir',
required=True,
help='directory to output files')
optional_test = test_parser.add_argument_group('optional arguments')
optional_test.add_argument('--cpus',
default=1,
type=int,
help='number of CPUs to use')
optional_test.add_argument('-h',
'--help',
action="help",
help="show help message")
# trim MSA
msa_parser = subparsers.add_parser(
'trim_msa',
conflict_handler='resolve',
formatter_class=CustomHelpFormatter,
help='Trim an untrimmed MSA file based on a mask.',
)
required_msa = msa_parser.add_argument_group('required named arguments')
required_msa.add_argument('--untrimmed_msa',
required=True,
help="untrimmed MSA file")
required_msa.add_argument('--output', required=True, help='output file')
mutual_trim_msa = msa_parser.add_argument_group(
'mutually exclusive required arguments')
mutex_msa_group = mutual_trim_msa.add_mutually_exclusive_group(
required=True)
mutex_msa_group.add_argument('--mask_file',
help="mask file to use for trimming the MSA")
mutex_msa_group.add_argument(
'--reference_mask',
choices=['arc', 'bac'],
help="reference mask already present in GTDB-Tk")
optional_msa = msa_parser.add_argument_group('optional arguments')
optional_msa.add_argument('-h',
'--help',
action="help",
help="show help message")
# export msa
export_msa_parser = subparsers.add_parser(
'export_msa',
conflict_handler='resolve',
formatter_class=CustomHelpFormatter,
help='Export the untrimmed archaeal or bacterial MSA file.',
)
required_export_msa = export_msa_parser.add_argument_group(
'required named arguments')
required_export_msa.add_argument('--domain',
required=True,
choices=['arc', 'bac'],
help="select domain to download")
required_export_msa.add_argument('--output',
required=True,
help='output file')
optional_export_msa = export_msa_parser.add_argument_group(
'optional arguments')
optional_export_msa.add_argument('-h',
'--help',
action="help",
help="show help message")
# verify install
check_install_parser = subparsers.add_parser(
'check_install',
conflict_handler='resolve',
formatter_class=CustomHelpFormatter,
help='Verify if all gtdb data files are present to run GTDB-Tk.',
)
optional_check_install = check_install_parser.add_argument_group(
'optional arguments')
optional_check_install.add_argument('-h',
'--help',
action="help",
help="show help message")
# -------------------------------------------------
# get and check options
args = None
if len(sys.argv) == 1:
print_help()
sys.exit(0)
elif sys.argv[1] in {'-v', '--v', '-version', '--version'}:
print("gtdbtk: version %s %s %s" %
(__version__, __copyright__, __author__))
sys.exit(0)
elif sys.argv[1] in {'-h', '--h', '-help', '--help'}:
print_help()
sys.exit(0)
else:
args = parser.parse_args()
# setup logger
logger_setup(args.out_dir if hasattr(args, 'out_dir') else None,
"gtdbtk.log", "GTDB-Tk", __version__, False,
hasattr(args, 'debug') and args.debug)
logger = logging.getLogger('timestamp')
# -------------------------------------------------
# do what we came here to do
try:
gt_parser = OptionsParser(__version__)
if False:
import cProfile
cProfile.run('gt_parser.parseOptions(args)', 'prof')
else:
gt_parser.parse_options(args)
except SystemExit:
sys.stdout.write('\n')
sys.stdout.flush()
logger.error('Controlled exit resulting from early termination.')
sys.exit(1)
except KeyboardInterrupt:
sys.stdout.write('\n')
sys.stdout.flush()
logger.error('Controlled exit resulting from interrupt signal.')
sys.exit(1)
except GTDBTkExit as e:
sys.stdout.write('\n')
sys.stdout.flush()
if len(str(e)) > 0:
logger.error('{}'.format(e))
logger.error(
'Controlled exit resulting from an unrecoverable error or warning.'
)
sys.exit(1)
except (GTDBTkException, BioLibError) as e:
sys.stdout.write('\n')
sys.stdout.flush()
msg = 'Controlled exit resulting from an unrecoverable error or warning.\n\n'
msg += '=' * 80 + '\n'
msg += 'EXCEPTION: {}\n'.format(type(e).__name__)
msg += ' MESSAGE: {}\n'.format(e)
msg += '_' * 80 + '\n\n'
msg += traceback.format_exc()
msg += '=' * 80
logger.error(msg)
sys.exit(1)
except Exception as e:
sys.stdout.write('\n')
sys.stdout.flush()
msg = 'Uncontrolled exit resulting from an unexpected error.\n\n'
msg += '=' * 80 + '\n'
msg += 'EXCEPTION: {}\n'.format(type(e).__name__)
msg += ' MESSAGE: {}\n'.format(e)
msg += '_' * 80 + '\n\n'
msg += traceback.format_exc()
msg += '=' * 80
logger.error(msg)
sys.exit(1)
