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yangao07 / abPOA

abPOA: an SIMD-based C library for fast partial order alignment using adaptive band
MIT License
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Segmentation fault error #52

Closed Goatofmountain closed 10 months ago

Goatofmountain commented 11 months ago

Hi Yan, I want to use abPOA with my ONT data to make multisequence alignment, but it comes out with a "Segmentation fault" error, with empty output. Here is my cmd abpoa -r 1 -S Test.fasta > Test.MSA.fasta and my test data file Test.zip

I wonder if abPOA is not fit for data with too many long read sequence when making MSA ?

Thank you. KT

yangao07 commented 11 months ago

Seems like your sequences are very long and divergent. I didn't see the seg fault but abpoa uses more than 512G memory even with the seeding mode enabled. For this case, I suggest you do some pre-processing and split the sequences into smaller regions, and apply abpoa for each region.

Goatofmountain commented 10 months ago

Thank you for your suggestion. After splitting the reads, the program worked fine, and the result was similar to what I expected. Useful tool, thanks again !