IndexError: list index out of range for torch.load(glob.glob(prot_1)[0])

[XueWang2019]

Dear Sir/Madam,

My update:
As I don't have the completed dataset, I guess the original issue comes from below reasons:

1. npy_file_new(human_dataset).npy has 22217 data
2. Current available human data is only 4444+1111=5555
   Above causes the below problem. Please feel free to correct me. Thanks.

Original issue:
I am running this project on google colab. This might not be an issue, but I don't know how to solve it.
There is a problem showing as : IndexError: list index out of range.
The part of result as:
GCNN Loaded Training on 4444 samples..... 15657 first prot is /content/gdrive/MyDrive/PPI_GNN/PPI_GNN/human_features/processed/3AIH.pt [] 15657 Second prot is /content/gdrive/MyDrive/PPI_GNN/PPI_GNN/human_features/processed/1DEV.pt Traceback (most recent call last): File "train.py", line 97, in <module> train(model, device, trainloader, optimizer, epoch+1) File "train.py", line 45, in train for count,(prot_1, prot_2, label) in enumerate(trainloader): File "/usr/local/lib/python3.7/dist-packages/torch/utils/data/dataloader.py", line 530, in __next__ data = self._next_data() File "/usr/local/lib/python3.7/dist-packages/torch/utils/data/dataloader.py", line 570, in _next_data data = self._dataset_fetcher.fetch(index) # may raise StopIteration File "/usr/local/lib/python3.7/dist-packages/torch/utils/data/_utils/fetch.py", line 49, in fetch data = [self.dataset[idx] for idx in possibly_batched_index] File "/usr/local/lib/python3.7/dist-packages/torch/utils/data/_utils/fetch.py", line 49, in <listcomp> data = [self.dataset[idx] for idx in possibly_batched_index] File "/usr/local/lib/python3.7/dist-packages/torch/utils/data/dataset.py", line 471, in __getitem__ return self.dataset[self.indices[idx]] File "/content/gdrive/MyDrive/PPI_GNN/PPI_GNN/data_prepare.py", line 41, in __getitem__ prot_1 = torch.load(glob.glob(prot_1)[0]) IndexError: list index out of range

The error comes from the code:
def __getitem__(self, index): prot_1 = os.path.join(self.processed_dir, self.protein_1[index]+".pt") print(index) print(f'first prot is {prot_1}') print(glob.glob('prot_1')) prot_2 = os.path.join(self.processed_dir, self.protein_2[index]+".pt") print(index) print(f'Second prot is {prot_2}') prot_1 = torch.load(glob.glob(prot_1)[0]) print(f'Here lies {glob.glob(prot_2)}') prot_2 = torch.load(glob.glob(prot_2)[0]) print(torch.tensor(self.label[index])) return prot_1, prot_2, torch.tensor(self.label[index])

It seems that glob.glob('prot_1') is null. How to solve this problem?
Thanks in advance.

[yangyangdotcom]

I go the same problem and fixed it by replacing the processed folder with this https://drive.google.com/file/d/1mpMB2Gu6zH6W8fZv-vGwTj_mmeitIV2-/view?usp=sharing. Hope it solves your problem

[HajerBashir]

@yangyangdotcom the link is not working ??