Getting error in the GTDB step.

Open ankurnaqib opened this issue 3 months ago • 1 comments

Hi,

I am getting an error while running the GTDB step. I am attaching the log file. It seems like Prodigal failed due to an error "AttributeError: module 'numpy' has no attribute 'bool'". Please help. Thank you.

gtdbtk-run.log

Oct 17 '25 16:10 ankurnaqib

Which version of the workflow are you running? Can you also provide information on the environment in which you ran the command? Was it a docker/singularity container (if so, which image/version)? Or if you used a conda environment, please provide the result of the conda export -n environment_name command. I suspect that your environment has a mismatch in the versions of some of the python packages used for that step.

Nov 13 '25 05:11 bnovak32