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WGLab / DeepMod2

DNA 5mC methylation detection from Dorado or Guppy basecalled Oxford Nanopore reads
MIT License
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--model 'transformer_r10.4.1_5khz_v4.3' has error "UnboundLocalError: local variable 'model' referenced before assignment " #24

Open kerenzhou062 opened 4 months ago

kerenzhou062 commented 4 months ago

when running deepmod2 detect --model 'transformer_r10.4.1_5khz_v4.3', it throws error like:

Traceback (most recent call last): File "/hpcf/authorized_apps/rhel8_apps/deepmod2/install/deepmod2-env2/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap self.run() File "/hpcf/authorized_apps/rhel8_apps/deepmod2/install/deepmod2-env2/lib/python3.10/multiprocessing/process.py", line 108, in run self._target(*self._args, **self._kwargs) File "/research/rgs01/applications/hpcf/authorized_apps/rhel8_apps/deepmod2/vendor/DeepMod2/src/detect.py", line 419, in process model, model_config=get_model(params) File "/research/rgs01/applications/hpcf/authorized_apps/rhel8_apps/deepmod2/vendor/DeepMod2/src/utils.py", line 108, in get_model model.load_state_dict(checkpoint['model_state_dict']) UnboundLocalError: local variable 'model' referenced before assignment`

umahsn commented 4 months ago

Hi,

Are you using the latest commit? This bug was fixed in commit 2f7c90daf463a289466c40ff1dac606503cf5f77, so if you use the latest version you should not have this error. Please use git pull command within DeepMod2 repository to pull the latest changes to the code.

Best, Umair