offline tool issue with the training
Closed this issue · 2 comments
Hello,
I am currently trying to run your tool with the docker container and I am facing an issue at the training step.
Here is the command line that I use:
/shared/projects/seabioz/softwares/CLEAN/clean-1.0.1.sif python ./scripts/train-supconH.py --training_data split100 --model_name split100_supconH --epoch 4100 --n_pos 9 --n_neg 30 -T 0.1
And here is the error I get:
Traceback (most recent call last): File "/shared/projects/seabioz/softwares/CLEAN/./scripts/train-supconH.py", line 139, in <module> main() File "/shared/projects/seabioz/softwares/CLEAN/./scripts/train-supconH.py", line 118, in main train_loss = train(model, args, epoch, train_loader, File "/shared/projects/seabioz/softwares/CLEAN/./scripts/train-supconH.py", line 50, in train for batch, data in enumerate(train_loader): File "/usr/local/lib/python3.10/site-packages/torch/utils/data/dataloader.py", line 634, in __next__ data = self._next_data() File "/usr/local/lib/python3.10/site-packages/torch/utils/data/dataloader.py", line 678, in _next_data data = self._dataset_fetcher.fetch(index) # may raise StopIteration File "/usr/local/lib/python3.10/site-packages/torch/utils/data/_utils/fetch.py", line 51, in fetch data = [self.dataset[idx] for idx in possibly_batched_index] File "/usr/local/lib/python3.10/site-packages/torch/utils/data/_utils/fetch.py", line 51, in <listcomp> data = [self.dataset[idx] for idx in possibly_batched_index] File "/usr/local/lib/python3.10/site-packages/CLEAN-0.1-py3.10.egg/CLEAN/dataloader.py", line 105, in __getitem__ File "/usr/local/lib/python3.10/site-packages/torch/serialization.py", line 791, in load with _open_file_like(f, 'rb') as opened_file: File "/usr/local/lib/python3.10/site-packages/torch/serialization.py", line 271, in _open_file_like return _open_file(name_or_buffer, mode) File "/usr/local/lib/python3.10/site-packages/torch/serialization.py", line 252, in __init__ super().__init__(open(name, mode)) FileNotFoundError: [Errno 2] No such file or directory: './data/esm_data/P32143_6.pt'
It's like a pt file was missing but I downloaded them with your scripts so I don't get what could be missing?
The P32143_6.pt was changed from P32143. I got this error too...In 1.0.1 version, the utils.py does not have the function of "mutate_single_seq_ECs", I guess the error was due to this? Have you fixed this error?
Yes, if an EC number only has one sequence (likely the case for P32143 here), it needs to be "mutated" (randomly masked from ESM-1b's view) so that it is possible to sample positive for the anchor. Please make sure that you have followed the instructions for the step that involves mutate_single_seq_ECs(train_file). Let us know if there is any further questions.