I use Casanovo 3.5.0 with model "casanovo_massivekb.ckpt" in denovo mode to predict on my own mgf file. I use my own config.yaml, and only changed "precursor_mass_tol: 10", "min_peptide_len: 4" and "predict_batch_size: 512". The following error occured:
"Predicting DataLoader 0: 91%|████████████████████████████████████████████▋ | 449/493 [24:24:58<2:23:33, 195.76s/it]Traceback (most recent call last):
File "D:\miniconda3\lib\runpy.py", line 197, in _run_module_as_main
return _run_code(code, main_globals, None,
File "D:\miniconda3\lib\runpy.py", line 87, in _run_code
exec(code, run_globals)
File "D:\miniconda3\Scripts\casanovo.exe\__main__.py", line 7, in <module>
File "D:\miniconda3\lib\site-packages\click\core.py", line 1157, in __call__
return self.main(*args, **kwargs)
File "D:\miniconda3\lib\site-packages\click\core.py", line 1078, in main
rv = self.invoke(ctx)
File "D:\miniconda3\lib\site-packages\click\core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "D:\miniconda3\lib\site-packages\click\core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "D:\miniconda3\lib\site-packages\casanovo\casanovo.py", line 166, in main
model_runner.predict(peak_path, model, config, writer)
File "D:\miniconda3\lib\site-packages\casanovo\denovo\model_runner.py", line 46, in predict
_execute_existing(peak_path, model_filename, config, False, out_writer)
File "D:\miniconda3\lib\site-packages\casanovo\denovo\model_runner.py", line 170, in _execute_existing
run_trainer(model, loaders.test_dataloader())
File "D:\miniconda3\lib\site-packages\pytorch_lightning\trainer\trainer.py", line 892, in predict
return call._call_and_handle_interrupt(
File "D:\miniconda3\lib\site-packages\pytorch_lightning\trainer\call.py", line 38, in _call_and_handle_interrupt
return trainer_fn(*args, **kwargs)
File "D:\miniconda3\lib\site-packages\pytorch_lightning\trainer\trainer.py", line 938, in _predict_impl
results = self._run(model, ckpt_path=self.ckpt_path)
File "D:\miniconda3\lib\site-packages\pytorch_lightning\trainer\trainer.py", line 1112, in _run
results = self._run_stage()
File "D:\miniconda3\lib\site-packages\pytorch_lightning\trainer\trainer.py", line 1190, in _run_stage
return self._run_predict()
File "D:\miniconda3\lib\site-packages\pytorch_lightning\trainer\trainer.py", line 1244, in _run_predict
return self.predict_loop.run()
File "D:\miniconda3\lib\site-packages\pytorch_lightning\loops\loop.py", line 199, in run
self.advance(*args, **kwargs)
File "D:\miniconda3\lib\site-packages\pytorch_lightning\loops\dataloader\prediction_loop.py", line 100, in advance
dl_predictions, dl_batch_indices = self.epoch_loop.run(
File "D:\miniconda3\lib\site-packages\pytorch_lightning\loops\loop.py", line 199, in run
self.advance(*args, **kwargs)
File "D:\miniconda3\lib\site-packages\pytorch_lightning\loops\epoch\prediction_epoch_loop.py", line 100, in advance
self._predict_step(batch, batch_idx, dataloader_idx)
File "D:\miniconda3\lib\site-packages\pytorch_lightning\loops\epoch\prediction_epoch_loop.py", line 129, in _predict_step
predictions = self.trainer._call_strategy_hook("predict_step", *step_kwargs.values())
File "D:\miniconda3\lib\site-packages\pytorch_lightning\trainer\trainer.py", line 1494, in _call_strategy_hook
output = fn(*args, **kwargs)
File "D:\miniconda3\lib\site-packages\pytorch_lightning\strategies\strategy.py", line 408, in predict_step
return self.model.predict_step(*args, **kwargs)
File "D:\miniconda3\lib\site-packages\casanovo\denovo\model.py", line 807, in predict_step
self.forward(batch[0], batch[1]),
File "D:\miniconda3\lib\site-packages\casanovo\denovo\model.py", line 195, in forward
return self.beam_search_decode(
File "D:\miniconda3\lib\site-packages\casanovo\denovo\model.py", line 267, in beam_search_decode
self._cache_finished_beams(
File "D:\miniconda3\lib\site-packages\casanovo\denovo\model.py", line 534, in _cache_finished_beams
heapadd(
ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
Predicting DataLoader 0: 91%|█████████ | 449/493 [24:27:51<2:23:50, 196.15s/it]"
wsnoble
commented
4 months ago
Hi Sir,
I use Casanovo 3.5.0 with model "casanovo_massivekb.ckpt" in denovo mode to predict on my own mgf file. I use my own config.yaml, and only changed "precursor_mass_tol: 10", "min_peptide_len: 4" and "predict_batch_size: 512". The following error occured:
Where might this error come from? Thanks!
Best regards