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raja-appuswamy / accel-align-release

A fast seed-embed-extend based sequence mapper and aligner
MIT License
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Segmentation fault with large genomes #24

Open dinhdiep opened 2 years ago

dinhdiep commented 2 years ago

Dear authors,

Thank you for creating accel-aligner. It is very fast and sensitive in my tests.

I have been trying to apply accel-aligner to bisulfite sequencing reads and was able to successfully aligned reads. However, as bisulfite reads must be aligned to both the converted forward and converted reverse complement DNA references, I thought about generating an index that is comprised of both references. However, I would get segmentation fault errors when running the aligner against the combined references whereas I do not have this problem when mapping against each reference separately.

Is this a problem caused by a limitation in the size of the reference index?

Best,

Dinh

raja-appuswamy commented 2 years ago

hey Dinh, Thanks for using Accel Align. Could you please give us step by step information about how you prepare the combined reference? Perhaps scripts to do it if you already have it? We would like to reproduce the error on our side to see what is wrong.

Raja

dinhdiep commented 2 years ago

Please see the attached shell script for generating this error! generate_accel_align_test.txt