-
Notifications
You must be signed in to change notification settings - Fork 5
Open
Description
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!
Metadata
Metadata
Assignees
Labels
No labels