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Segmentation fault with large reference genome #57

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TomofumiSaka opened this issue Sep 8, 2023 · 1 comment
Open

Segmentation fault with large reference genome #57

TomofumiSaka opened this issue Sep 8, 2023 · 1 comment

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@TomofumiSaka
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When I used large reference file (3.6Gbp) , DRAGMAP outputted the below warning message while building .

Increasing seed interval to1.156789 for long reference

With this reference hash table, DRAGMAP generated seeds to wrong place and exited by segmentation fault.
I don't know how to fix this bug but I was able to avoid this bug by increase memory usage by --ht-mem-limit 512GB option.

@TomofumiSaka
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As reported in this issue #33 , large reference files can not be used with DRAGMAP.
I fixed like this pull request #55 .

Then, I encountered this segmentation fault bug.

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