pydantic.dev/2.6/v/missing

[WUD2018]

I have downloaded and installed the gtdb-tk v 2.3.0 the via mamba as suggested by the https://ecogenomics.github.io/GTDBTk/installing/bioconda.html

However, when I run the command, 'pydanic.dev.error' occured. Could you please kindly help me out? thanks.

[2024-02-03 10:20:10] INFO: GTDB-Tk v2.3.0
[2024-02-03 10:20:10] INFO: gtdbtk classify_wf --cpus 40 --genome_dir ./ --out_dir ./AnimFece80_gtdbtk2.3_output --extension fa --prefix AnimFece80 --min_af 0.80 --skip_ani_screen
[2024-02-03 10:20:10] INFO: Using GTDB-Tk reference data version r214: /home/disk1/DataBase/GTDBTK-2.3.0/release214
[2024-02-03 10:20:10] 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/2.6/v/missing
command_line
Field required [type=missing, input_value={'steps': []}, input_type=dict]
For further information visit https://errors.pydantic.dev/2.6/v/missing
database_version
Field required [type=missing, input_value={'steps': []}, input_type=dict]
For further information visit https://errors.pydantic.dev/2.6/v/missing
database_path
Field required [type=missing, input_value={'steps': []}, input_type=dict]
For further information visit https://errors.pydantic.dev/2.6/v/missing
output_dir
Field required [type=missing, input_value={'steps': []}, input_type=dict]
For further information visit https://errors.pydantic.dev/2.6/v/missing
path
Field required [type=missing, input_value={'steps': []}, input_type=dict]
For further information visit https://errors.pydantic.dev/2.6/v/missing

---

Traceback (most recent call last):
File "/home/disk1/Anaconda3/envs/mamba/envs/gtdbtk-2.3.0/lib/python3.8/site-packages/gtdbtk/main.py", line 100, in main
gt_parser = OptionsParser(version,
File "/home/disk1/Anaconda3/envs/mamba/envs/gtdbtk-2.3.0/lib/python3.8/site-packages/gtdbtk/main.py", line 86, in init
self.stage_logger = StageLogger()
File "/home/disk1/Anaconda3/envs/mamba/envs/gtdbtk-2.3.0/lib/python3.8/site-packages/gtdbtk/files/stage_logger.py", line 172, in new
StageLogger.instance = StageLogger.__StageLogger(steps=[])
File "/home/disk1/Anaconda3/envs/mamba/envs/gtdbtk-2.3.0/lib/python3.8/site-packages/pydantic/main.py", line 171, in init
self.pydantic_validator.validate_python(data, self_instance=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/2.6/v/missing
command_line
Field required [type=missing, input_value={'steps': []}, input_type=dict]
For further information visit https://errors.pydantic.dev/2.6/v/missing
database_version
Field required [type=missing, input_value={'steps': []}, input_type=dict]
For further information visit https://errors.pydantic.dev/2.6/v/missing
database_path
Field required [type=missing, input_value={'steps': []}, input_type=dict]
For further information visit https://errors.pydantic.dev/2.6/v/missing
output_dir
Field required [type=missing, input_value={'steps': []}, input_type=dict]
For further information visit https://errors.pydantic.dev/2.6/v/missing
path
Field required [type=missing, input_value={'steps': []}, input_type=dict]
For further information visit https://errors.pydantic.dev/2.6/v/missing

Environment

• Installed via pip (include the output of pip list)
• Using a conda environment (include the output of conda list && conda list --revisions)
• Using a Docker container (include the IMAGE ID of the container)

Server information

• CPU: grep -m 1 "^model name" /proc/cpuinfo && grep -c "^processor" /proc/cpuinfo
• RAM: grep "^MemTotal" /proc/meminfo
• OS: cat /etc/os-release

Debugging information

• gtdbtk.log has been included (drag and drop the file to upload).
• Genomes have been included (if possible, and there are few).

Additional comments

[pchaumeil]

Hello,
Please download the latest version of GTDB-Tk ( 2.3.2). This should fix this issue.

Cheers,
Pierre