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list index out of range #13
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Hi @yuehua-Song666, many thanks for your interest! And apologies for this very delayed response.
Have you created the processed dataset yourself from the raw RNAsolo PDB files? Or have you downloaded it from our link: https://drive.google.com/file/d/1gcUUaRxbGZnGMkLdtVwAILWVerVCbu4Y/view?usp=sharing
I think the index error could be happening if you have created the processed dataset by yourself and there are fewer entries/samples in the new processed dataset than there were when I created the splits. Could you check whether this is the case? Essentially, index out of range means that the list of indexes in the das_split contains one or more indexes that are far too large to be able to correctly index the processed data list. It is likely that the processed data list has length N, but the index value is something like N + x > N, so it leads to an index out of range error.
We have provided two splits used in our experiments in the
Let me know if this is helpful. |
Hi @yuehua-Song666, I recently updated the instructions for preparing the data and for reproducing our splits for benchmarking: #16 Somebody else told me that RNAsolo was no longer allowing downloading older versions based on date cutoffs, and I suspect the issues you were facing can be due to the same reason. If you try the new data instructions in the README, I think it should work. Let me know how it goes! |
Hi authors, Thank you so much for such an useful reply! I figured it out. =) Thanks a lot, |
Dear authors,
Thank you so much for such great work. I'm really interested in it.
I got an issue here, after getting processed.pt, I tried to run main.py. It uses das_split.pt to split the data into train, val and test, right? But I got an "index out of range" error. I wonder if you have any clues why this happened? By the way, I saw under the data folder, you have three '_split.pt' files, can you please tell me the difference between them?
Error log:
46 Traceback (most recent call last):
47 File "/home/yjwang/geometric-rna-design/main.py", line 246, in
48 main(config, device)
49 File "/home/yjwang/geometric-rna-design/main.py", line 39, in main
50 train_list, val_list, test_list = get_data_splits(config, split_type=config.split)
51 File "/home/yjwang/geometric-rna-design/main.py", line 119, in get_data_splits
52 train_list = index_list_by_indices(data_list, train_idx_list)
53 File "/home/yjwang/geometric-rna-design/main.py", line 113, in index_list_by_indices
54 return [lst[index] for index in indices]
55 File "/home/yjwang/geometric-rna-design/main.py", line 113, in
56 return [lst[index] for index in indices]
57 IndexError: list index out of range
Thanks in advance,
yuehua
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