size of tensor must match error

[Yogesh1-11]

Hi i am using diffdock docker image with the following command, but getting this error . i tried with conda as well but stuck with same error. can you please point the mistake?

(diffdock) appuser@dcb31e1e799d:~/DiffDock$ python -m inference --config default_inference_args.yaml --protein_path /data/protein.pdb --ligand /data/ligand.sdf
/home/appuser/micromamba/envs/diffdock/lib/python3.9/site-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module.
warnings.warn(
Generating ESM language model embeddings
Processing 1 of 1 batches (1 sequences)
0it [00:00, ?it/s]/home/appuser/DiffDock/datasets/parse_chi.py:91: RuntimeWarning: invalid value encountered in cast
Y = indices.astype(int)
Skipping complex_0 because of the error:
Sizes of tensors must match except in dimension 1. Expected size 1514 but got size 1022 for tensor number 1 in the list.
[2025-Jan-11 02:32:54 UTC] WARNING -The test dataset did not contain complex_0 for /data/ligand.sdf and /data/protein.pdb. We are skipping this complex.
1it [00:01, 1.13s/it]
[2025-Jan-11 02:32:54 UTC] WARNING -
Failed for 0 / 1 complexes.
Skipped 1 / 1 complexes.

[veon8]

Has it been solved? I also had the same problem

[wdlingit]

It seems that 1022 is some kind of regular number. Me got the message (protein names masked) when docking one ligand against more than 100 pdb files. After some check, those skipped proteins are exactly those proteins longer than 1022aa.

Skipping MASKPROT because of the error:
Sizes of tensors must match except in dimension 1. Expected size 1118 but got size 1022 for tensor number 1 in the list.
Skipping MASKPROT because of the error:
Sizes of tensors must match except in dimension 1. Expected size 1106 but got size 1022 for tensor number 1 in the list.
Skipping MASKPROT because of the error:
Sizes of tensors must match except in dimension 1. Expected size 1140 but got size 1022 for tensor number 1 in the list.
Skipping MASKPROT because of the error:
Sizes of tensors must match except in dimension 1. Expected size 1151 but got size 1022 for tensor number 1 in the list.
Skipping MASKPROT because of the error:
Sizes of tensors must match except in dimension 1. Expected size 1045 but got size 1022 for tensor number 1 in the list.
Skipping MASKPROT because of the error:
Sizes of tensors must match except in dimension 1. Expected size 1196 but got size 1022 for tensor number 1 in the list.
Skipping MASKPROT because of the error:
Sizes of tensors must match except in dimension 1. Expected size 1041 but got size 1022 for tensor number 1 in the list.

[wdlingit]

Now I got it. #199 has some discussion on this.