2026-03-22 06:11:16 DEBUG:busco.run_BUSCO	Command line: /usr/local/bin/busco --download_path busco_downloads --offline -i EGAPx_Test_Assembly_EGAPx_Test_Assembly.prot.fa --out output --mode proteins --cpu 24 --lineage_dataset arthropoda_odb10 --tar
2026-03-22 06:11:16 INFO:busco.run_BUSCO	***** Start a BUSCO v5.7.1 analysis, current time: 03/22/2026 06:11:16 *****
2026-03-22 06:11:16 DEBUG:busco.ConfigManager	Getting config file
2026-03-22 06:11:16 INFO:busco.ConfigManager	Configuring BUSCO with local environment
2026-03-22 06:11:16 INFO:busco.BuscoConfig	Running proteins mode
2026-03-22 06:11:16 DEBUG:busco.BuscoConfig	State of BUSCO config before run:
2026-03-22 06:11:16 DEBUG:busco.BuscoConfig	{'_allow_no_value': False,
 '_comment_prefixes': ('#', ';'),
 '_converters': <configparser.ConverterMapping object at 0x14b9bc7358e0>,
 '_defaults': {},
 '_delimiters': ('=', ':'),
 '_dict': <class 'dict'>,
 '_empty_lines_in_values': True,
 '_inline_comment_prefixes': (),
 '_input_filepath': 'EGAPx_Test_Assembly_EGAPx_Test_Assembly.prot.fa',
 '_interpolation': <configparser.BasicInterpolation object at 0x14b9c4361790>,
 '_mode': 'proteins',
 '_optcre': re.compile('\n        (?P<option>.*?)                    # very permissive!\n        \\s*(?P<vi>=|:)\\s*              # any number of space/tab,\n                                           # followed by any of t, re.VERBOSE),
 '_proxies': {'DEFAULT': <Section: DEFAULT>,
              'augustus': <Section: augustus>,
              'bbtools': <Section: bbtools>,
              'busco_run': <Section: busco_run>,
              'etraining': <Section: etraining>,
              'gff2gbSmallDNA.pl': <Section: gff2gbSmallDNA.pl>,
              'hmmsearch': <Section: hmmsearch>,
              'makeblastdb': <Section: makeblastdb>,
              'metaeuk': <Section: metaeuk>,
              'miniprot': <Section: miniprot>,
              'new_species.pl': <Section: new_species.pl>,
              'optimize_augustus.pl': <Section: optimize_augustus.pl>,
              'prodigal': <Section: prodigal>,
              'sepp': <Section: sepp>,
              'tblastn': <Section: tblastn>},
 '_sections': {'augustus': {'command': '', 'path': ''},
               'bbtools': {'command': '', 'path': ''},
               'busco_run': {'auto-lineage': 'False',
                             'auto-lineage-euk': 'False',
                             'auto-lineage-prok': 'False',
                             'batch_mode': 'False',
                             'cpu': '24',
                             'datasets_version': 'odb10',
                             'download_base_url': 'https://busco-data.ezlab.org/v5/data/',
                             'download_path': '/gscratch/scrubbed/lhs3/snow_annotation/work/3e/0661da5f429546dd49b244b985a19a/busco_downloads',
                             'force': 'False',
                             'in': '/gscratch/scrubbed/lhs3/snow_annotation/work/3e/0661da5f429546dd49b244b985a19a/EGAPx_Test_Assembly_EGAPx_Test_Assembly.prot.fa',
                             'lineage_dataset': 'arthropoda_odb10',
                             'main_out': '/gscratch/scrubbed/lhs3/snow_annotation/work/3e/0661da5f429546dd49b244b985a19a/output',
                             'mode': 'proteins',
                             'offline': 'True',
                             'opt-out-run-stats': 'False',
                             'out': 'output',
                             'out_path': '/gscratch/scrubbed/lhs3/snow_annotation/work/3e/0661da5f429546dd49b244b985a19a',
                             'quiet': 'False',
                             'restart': 'False',
                             'skip_bbtools': 'False',
                             'tar': 'True',
                             'use_augustus': 'False',
                             'use_metaeuk': 'False',
                             'use_miniprot': 'False'},
               'etraining': {'command': '', 'path': ''},
               'gff2gbSmallDNA.pl': {'command': '', 'path': ''},
               'hmmsearch': {'command': '', 'path': ''},
               'makeblastdb': {'command': '', 'path': ''},
               'metaeuk': {'command': '', 'path': ''},
               'miniprot': {'command': '', 'path': ''},
               'new_species.pl': {'command': '', 'path': ''},
               'optimize_augustus.pl': {'command': '', 'path': ''},
               'prodigal': {'command': '', 'path': ''},
               'sepp': {'command': '', 'path': ''},
               'tblastn': {'command': '', 'path': ''}},
 '_strict': True,
 'conf_file': 'local environment',
 'default_section': 'DEFAULT',
 'downloader': <busco.BuscoDownloadManager.BuscoDownloadManager object at 0x14b9b230b410>,
 'main_out': '/gscratch/scrubbed/lhs3/snow_annotation/work/3e/0661da5f429546dd49b244b985a19a/output',
 'params': {'augustus_parameters': None,
            'augustus_species': None,
            'auto-lineage': False,
            'auto-lineage-euk': False,
            'auto-lineage-prok': False,
            'config_file': None,
            'contig_break': None,
            'cpu': 24,
            'datasets_version': None,
            'download': '==SUPPRESS==',
            'download_base_url': None,
            'download_path': 'busco_downloads',
            'evalue': None,
            'force': False,
            'help': '==SUPPRESS==',
            'in': 'EGAPx_Test_Assembly_EGAPx_Test_Assembly.prot.fa',
            'limit': None,
            'lineage_dataset': 'arthropoda_odb10',
            'list_datasets': '==SUPPRESS==',
            'long': False,
            'metaeuk_parameters': None,
            'metaeuk_rerun_parameters': None,
            'mode': 'proteins',
            'offline': True,
            'opt-out-run-stats': False,
            'out': 'output',
            'out_path': None,
            'quiet': False,
            'restart': False,
            'scaffold_composition': False,
            'skip_bbtools': False,
            'tar': True,
            'use_augustus': False,
            'use_metaeuk': False,
            'use_miniprot': False,
            'version': '==SUPPRESS=='},
 'run_stats': {'cpu': 24,
               'download_path': 'user-specified',
               'input_file_size': 12393907,
               'lineage_dataset': ['arthropoda_odb10'],
               'mode': 'proteins',
               'offline': True,
               'tar': True}}
2026-03-22 06:11:16 INFO:busco.BuscoRunner	Input file is /gscratch/scrubbed/lhs3/snow_annotation/work/3e/0661da5f429546dd49b244b985a19a/EGAPx_Test_Assembly_EGAPx_Test_Assembly.prot.fa
2026-03-22 06:11:16 WARNING:busco.BuscoConfig	The dataset you provided does not contain the file dataset.cfg and is not valid for BUSCO v4.0 or higher
2026-03-22 06:11:16 CRITICAL:busco.BuscoRunner	Unhandled exception occurred:
Traceback (most recent call last):
  File "/usr/lib/python3.12/configparser.py", line 767, in get
    value = d[option]
            ~^^^^^^^^
  File "/usr/lib/python3.12/collections/__init__.py", line 1015, in __getitem__
    return self.__missing__(key)            # support subclasses that define __missing__
           ^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.12/collections/__init__.py", line 1007, in __missing__
    raise KeyError(key)
KeyError: 'domain'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/lib/python3.12/dist-packages/busco/BuscoRunner.py", line 151, in run
    self.runner = AnalysisRunner(self.config)
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/dist-packages/busco/BuscoRunner.py", line 381, in __init__
    self.mode, self.domain = self.config.update_mode()
                             ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/dist-packages/busco/BuscoConfig.py", line 235, in update_mode
    domain = self.get("busco_run", "domain")
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.12/configparser.py", line 770, in get
    raise NoOptionError(option, section)
configparser.NoOptionError: No option 'domain' in section: 'busco_run'


2026-03-22 06:11:16 ERROR:busco.BuscoRunner	No option 'domain' in section: 'busco_run'
2026-03-22 06:11:16 DEBUG:busco.BuscoRunner	No option 'domain' in section: 'busco_run'
Traceback (most recent call last):
  File "/usr/lib/python3.12/configparser.py", line 767, in get
    value = d[option]
            ~^^^^^^^^
  File "/usr/lib/python3.12/collections/__init__.py", line 1015, in __getitem__
    return self.__missing__(key)            # support subclasses that define __missing__
           ^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.12/collections/__init__.py", line 1007, in __missing__
    raise KeyError(key)
KeyError: 'domain'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/lib/python3.12/dist-packages/busco/BuscoRunner.py", line 151, in run
    self.runner = AnalysisRunner(self.config)
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/dist-packages/busco/BuscoRunner.py", line 381, in __init__
    self.mode, self.domain = self.config.update_mode()
                             ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/dist-packages/busco/BuscoConfig.py", line 235, in update_mode
    domain = self.get("busco_run", "domain")
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.12/configparser.py", line 770, in get
    raise NoOptionError(option, section)
configparser.NoOptionError: No option 'domain' in section: 'busco_run'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/lib/python3.12/dist-packages/busco/run_BUSCO.py", line 74, in run
    runner.run()
  File "/usr/local/lib/python3.12/dist-packages/busco/BuscoLogger.py", line 62, in wrapped_func
    self.retval = func(*args, **kwargs)
                  ^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/dist-packages/busco/BuscoRunner.py", line 197, in run
    raise BatchFatalError(str(exc_value))
busco.Exceptions.BatchFatalError: No option 'domain' in section: 'busco_run'
2026-03-22 06:11:16 ERROR:busco.BuscoRunner	BUSCO analysis failed!
2026-03-22 06:11:16 ERROR:busco.BuscoRunner	Check the logs, read the user guide (https://busco.ezlab.org/busco_userguide.html), and check the BUSCO issue board on https://gitlab.com/ezlab/busco/issues

2026-03-22 06:11:16 DEBUG:urllib3.connectionpool	Starting new HTTPS connection (1): busco-data.ezlab.org:443
2026-03-22 06:11:16 DEBUG:urllib3.connectionpool	Starting new HTTPS connection (1): busco-data.ezlab.org:443
2026-03-22 06:11:17 DEBUG:urllib3.connectionpool	https://busco-data.ezlab.org:443 "PUT /upload/rundata20260322061116367704.txt HTTP/1.1" 201 0
2026-03-22 06:11:17 DEBUG:urllib3.connectionpool	https://busco-data.ezlab.org:443 "PUT /upload/rundata20260322061116367704.txt HTTP/1.1" 201 0
2026-03-22 06:11:17 DEBUG:busco.run_BUSCO	File uploaded successfully.