Hi @horikini Oh I’m so sorry, I thought this was corrected already but it appears to be still pending.
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Resolved! Current implementation of GTDB-Tk Classify genomes is broken (wrong default arguments) - #2 by wm75
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Resolved! GTDB-Tk bug · Issue #7980 · galaxyproject/tools-iuc · GitHub
Let’s close this topic out and redirect over to the single active tracking topic for this! 
Updated topic → "GTDB-Tk database" Galaxy Version 2.6.0+galaxy0