ERROR: Uncontrolled exit resulting from an unexpected error

[MonsterLaplace]

(gtdbtk) xb@zooeco-ESC8000A-E12:~/metagenome/database$ gtdbtk test --out_dir /mnt/z/xb/test
[2023-07-05 16:33:48] INFO: GTDB-Tk v2.3.0
[2023-07-05 16:33:48] INFO: gtdbtk test --out_dir /mnt/z/xb/metagenome/test
[2023-07-05 16:33:48] INFO: Using GTDB-Tk reference data version r214: /mnt/z/xb/database/db
[2023-07-05 16:33:48] ERROR: Uncontrolled exit resulting from an unexpected error.

================================================================================
EXCEPTION: ValidationError
MESSAGE: 6 validation errors for __StageLogger
version
Field required [type=missing, input_value={'steps': []}, input_type=dict]
For further information visit https://errors.pydantic.dev/2.0.1/v/missing
command_line
Field required [type=missing, input_value={'steps': []}, input_type=dict]
For further information visit https://errors.pydantic.dev/2.0.1/v/missing
database_version
Field required [type=missing, input_value={'steps': []}, input_type=dict]
For further information visit https://errors.pydantic.dev/2.0.1/v/missing
database_path
Field required [type=missing, input_value={'steps': []}, input_type=dict]
For further information visit https://errors.pydantic.dev/2.0.1/v/missing
output_dir
Field required [type=missing, input_value={'steps': []}, input_type=dict]
For further information visit https://errors.pydantic.dev/2.0.1/v/missing
path
Field required [type=missing, input_value={'steps': []}, input_type=dict]
For further information visit https://errors.pydantic.dev/2.0.1/v/missing

---

Traceback (most recent call last):
File "/mnt/z/xb/miniconda3/envs/gtdbtk/lib/python3.8/site-packages/gtdbtk/main.py", line 100, in main
gt_parser = OptionsParser(version,
File "/mnt/z/xb/miniconda3/envs/gtdbtk/lib/python3.8/site-packages/gtdbtk/main.py", line 86, in init
self.stage_logger = StageLogger()
File "/mnt/z/xb/miniconda3/envs/gtdbtk/lib/python3.8/site-packages/gtdbtk/files/stage_logger.py", line 172, in new
StageLogger.instance = StageLogger.__StageLogger(steps=[])
File "/mnt/z/xb/miniconda3/envs/gtdbtk/lib/python3.8/site-packages/pydantic/main.py", line 150, in init
pydantic_self.pydantic_validator.validate_python(data, self_instance=pydantic_self)
pydantic_core._pydantic_core.ValidationError: 6 validation errors for __StageLogger
version
Field required [type=missing, input_value={'steps': []}, input_type=dict]
For further information visit https://errors.pydantic.dev/2.0.1/v/missing
command_line
Field required [type=missing, input_value={'steps': []}, input_type=dict]
For further information visit https://errors.pydantic.dev/2.0.1/v/missing
database_version
Field required [type=missing, input_value={'steps': []}, input_type=dict]
For further information visit https://errors.pydantic.dev/2.0.1/v/missing
database_path
Field required [type=missing, input_value={'steps': []}, input_type=dict]
For further information visit https://errors.pydantic.dev/2.0.1/v/missing
output_dir
Field required [type=missing, input_value={'steps': []}, input_type=dict]
For further information visit https://errors.pydantic.dev/2.0.1/v/missing
path
Field required [type=missing, input_value={'steps': []}, input_type=dict]
For further information visit https://errors.pydantic.dev/2.0.1/v/missing

[GeoMicroSoares]

The same is happening to me as well using gtdbtk versions 2.3.0 and 2.2.6 - thanks in advance for any help!

[Sidduppal]

Getting the same error as well after doing a fresh install yesterday.
Looks similar to issue#258

[MonsterLaplace]

Problem solved, thank you for your quick response.

[GeoMicroSoares]

Hi there - FYI after this solve I was only able to run gtdtk after downgrading gsl to 2.6 - maybe that can be helpful for you! Thanks!

[pchaumeil]

Thanks for your feedback!

[kunaljaani]

Hi!
If someone is still struggling with this error, the following may help.

python -m pip install gtdbtk --upgrade #v2.3.2
conda env config vars set GTDBTK_DATA_PATH="/path/to/unarchived/gtdbtk/data"
or
export GTDBTK_DATA_PATH=/path/to/release/package/
restart your session