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labstructbioinf / pLM-BLAST

Detection of remote homology by comparison of protein language model representations
https://toolkit.tuebingen.mpg.de/tools/plmblast
MIT License
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ERROR in function filtering_db #20

Closed staszekdh closed 11 months ago

staszekdh commented 11 months ago

The following error occurs for this sequence:

SEQ >ACC80284.1 PetN family protein [Nostoc punctiforme PCC 73102] MEILTLGWVSLLVVFTWSIAMVVWGRNGL

ERROR


/home/nfs/kpawlicki/plmblast/pLM-BLAST/alntools/numeric.py:182: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  @numba.jit(fastmath=True, cache=True)
using column: sequence
  0%|                                                                                                                                                                           | 0/2 [00:00<?, ?it/s]
Traceback (most recent call last):
  File "/home/nfs/kpawlicki/plmblast/pLM-BLAST/scripts/plmblast.py", line 165, in <module>
    query_filedict = filtering_db(args, query_embs)
  File "/home/nfs/kpawlicki/plmblast/pLM-BLAST/scripts/plmblast.py", line 80, in filtering_db
    filedict = ds.local.chunk_cosine_similarity(
  File "/home/nfs/kpawlicki/plmblast/pLM-BLAST/alntools/density/local.py", line 252, in chunk_cosine_similarity
    scorestack = chunk_score(query, targets, stride = stride, kernel_size=kernel_size)
RuntimeError: The following operation failed in the TorchScript interpreter.
Traceback of TorchScript (most recent call last):
  File "/home/nfs/kpawlicki/plmblast/pLM-BLAST/alntools/density/local.py", line 328, in chunk_score
        num_targets: int = len(targets)
        scorestack: List[float] = list()
        query_kernels = sequence_to_filters(query, kernel_size=kernel_size,
                 ~~~~~~~~~~~~~~~~~~~ <--- HERE
                                                                                norm=True, with_padding=False)

  File "/home/nfs/kpawlicki/plmblast/pLM-BLAST/alntools/density/local.py", line 86, in sequence_to_filters
                        filt = protein.narrow(0, start, kernel_size).unsqueeze(0)
                        filter_list.append(filt)
        filters = th.cat(filter_list, 0)
           ~~~~~~ <--- HERE
        filters = filters.view(num_filters, 1, kernel_size, emb_size)
        # normalize filters
RuntimeError: torch.cat(): expected a non-empty list of Tensors