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GTDB-tk crashes when run twice with the same output directory #684

@fplazaonate

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@fplazaonate

Hi,

After a first execution, GTDB-tk v2.6.1 crashes when using the same output directory without cleaning it.

Here is the logging message:

[2026-01-09 11:40:03] INFO: Using GTDB-Tk reference data version r226: /biodatabank/annot_db/gtdb/release226/
[2026-01-09 11:40:03] ERROR: Uncontrolled exit resulting from an unexpected error.

================================================================================
EXCEPTION: TypeError
  MESSAGE: ANIScreenStep.__init__() got an unexpected keyword argument 'name'
________________________________________________________________________________

Traceback (most recent call last):
  File "gtdbtk_python313/lib/python3.13/site-packages/gtdbtk/__main__.py", line 100, in main
    gt_parser.parse_options(args)
    ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
  File "gtdbtk_python313/lib/python3.13/site-packages/gtdbtk/main.py", line 1088, in parse_options
    self.stage_logger.read_existing_steps()
    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^
  File "gtdbtk_python313/lib/python3.13/site-packages/gtdbtk/files/stage_logger.py", line 168, in read_existing_steps
    step_object = ANIScreenStep(**step)
TypeError: ANIScreenStep.__init__() got an unexpected keyword argument 'name'
================================================================================

Florian

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