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TypeError while aligning #27

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anna-pa-m opened this issue Jun 7, 2023 · 0 comments
Open

TypeError while aligning #27

anna-pa-m opened this issue Jun 7, 2023 · 0 comments

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@anna-pa-m
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anna-pa-m commented Jun 7, 2023

I am getting the following error while using caretta from the command line (I can provide the list of pdbs to reproduce the error if needed):

caretta-cli list_IPR000072_pdbs.dat 
Found 66 structure files
Found 66 protein structures 100%|
Computed invariants in 13.59 seconds
Found 66 structures with valid invariants 100%|
Aligning:   3%|███   
Traceback (most recent call last):

  File "/home/disat/amuntoni/miniconda3/bin/caretta-cli", line 127, in <module>
    app()

  File "/home/disat/amuntoni/miniconda3/bin/caretta-cli", line 108, in align
    multiple_alignment.align_from_structure_files(

  File "/home/disat/amuntoni/miniconda3/lib/python3.9/site-packages/caretta/multiple_alignment.py", line 519, in align_from_structure_files
    alignment = msa_class.multiple_align(

  File "/home/disat/amuntoni/miniconda3/lib/python3.9/site-packages/caretta/multiple_alignment.py", line 278, in multiple_align
    self.alignment = self.progressive_align(self.tree,

  File "/home/disat/amuntoni/miniconda3/lib/python3.9/site-packages/caretta/multiple_alignment.py", line 243, in progressive_align
    make_intermediate_node(node_1, node_2, node_int)

  File "/home/disat/amuntoni/miniconda3/lib/python3.9/site-packages/caretta/multiple_alignment.py", line 204, in make_intermediate_node
    score_matrix = final_sequences[n1].score_function(

  File "/home/disat/amuntoni/miniconda3/lib/python3.9/site-packages/caretta/multiple_alignment.py", line 332, in score_function
    aln_1, aln_2, score = dtw.smith_waterman(np.arange(score_matrix.shape[0]),

TypeError: expected UniTuple(int64 x 2), got None

Is it related to a "bad" PDB file? How can I spot it?
Thank you for your help!

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