Error in gtdbtk-2.3.0, de_novo_wf and test

GTDB-Tk
1

Please help me with this

[2023-07-04 15:04:09] INFO: GTDB-Tk v2.3.0
[2023-07-04 15:04:09] INFO: gtdbtk de_novo_wf --genome_dir 112fa --archaea --outgroup_taxon p__Thaumarchaeota --out_dir 07_drep_100_GUNC_pass_gtdbtk_denovo_out --cpus 32 -x fa

EXCEPTION: ValidationError
MESSAGE: 6 validation errors for __StageLogger
version
Field required [type=missing, input_value={‘steps’: []}, input_type=dict]
For further information visit
command_line
Field required [type=missing, input_value={‘steps’: []}, input_type=dict]
For further information visit Validation Errors - Pydantic
database_version
Field required [type=missing, input_value={‘steps’: []}, input_type=dict]
For further information visit Validation Errors - Pydantic
database_path
Field required [type=missing, input_value={‘steps’: []}, input_type=dict]
For further information visit
output_dir
Field required [type=missing, input_value={‘steps’: []}, input_type=dict]
For further information visit
path
Field required [type=missing, input_value={‘steps’: []}, input_type=dict]
For further information visit

2

Hi,
GTDB-Tk has been updated to v2.3.2 to fix a dependency with pydantic.
Please update GTDB-Tk to this new version to fix this issue

3

happy to see that!