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MIC-DKFZ / nnUNet

Apache License 2.0
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Command not found #2434

Open maggie-may-22 opened 3 months ago

maggie-may-22 commented 3 months ago

Hi, I have previously completed preprocessing, training and prediction and everything was working fine.

I have now created a new folder structure and restarted using different data. For some reason I am getting an error code that says the command is not found - i am doing the preprocessing and have tried both nnUNetv2_plan_and_preprocess and nnUNetv2_extract_fingerprint. I have also tried cloning the nnUNet repository as well as using as a standardised baseline.

Looking at the file paths in my image below, the folder named '001' contains 'data' folder, 'nnUNet' folder and the script I submitted.

For context, I have to run bash files through a HPC as my computer isn't powerful enough. I have attached a screenshot of my script and the error message.

Bash file Error
JackRio commented 2 months ago

Try upgrading your pip and setuptools library and then install.

Read the whole error logs the issue is with old pip and setuptools versions most likely.

maggie-may-22 commented 2 months ago

I am running through a HPC using the PuTTY SSH so I can't run any commands or upgrade directly from the terminal. I haven't been able to get the issue to go away and this is the only error file I get after running my script:

Collecting nnunetv2 Using cached https://files.pythonhosted.org/packages/e9/76/b07d94295b8680333c267420cb8fe68780c1f0330b01f83de221e14398f8/nnunetv2-2.0.tar.gz Complete output from command python setup.py egg_info: Traceback (most recent call last): File "", line 1, in File "/data1/pbs.9829022.pbs/pip-build-MXkLvm/nnunetv2/setup.py", line 1, in from setuptools import setup, find_namespace_packages ImportError: cannot import name find_namespace_packages

----------------------------------------

Command "python setup.py egg_info" failed with error code 1 in /data1/pbs.9829022.pbs/pip-build-MXkLvm/nnunetv2/ You are using pip version 9.0.1, however version 24.2 is available. You should consider upgrading via the 'pip install --upgrade pip' command. /var/spool/PBS/mom_priv/jobs/9829022.pbs.SC: line 18: nnUNetv2_plan_and_preprocess: command not found

Any ideas??