YosefLab / Cassiopeia

A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction
https://cassiopeia-lineage.readthedocs.io/en/latest/
MIT License
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Segmentation fault in cas.pp.align_sequences #246

Open peipp410 opened 1 month ago

peipp410 commented 1 month ago

Hello! I encountered the following error

joblib.externals.loky.process_executor.TerminatedWorkerError: A worker process managed by the executor was unexpectedly terminated. This could be caused by a segmentation fault while calling the function or by an excessive memory usage causing the Operating System to kill the worker.

in cas.pp.align_sequences when setting the gap_extend_penalty as a float number less then 1. I noticed that in our experiment, the Cas9 will cut a long sequence(about 200-300bp). Therefore, I want the gap extend penalty to be smaller so that it will record the alleles on two distant cutting sites that would otherwise be omitted by local alignment.