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BGI-Qingdao / TGS-GapCloser

A gap-closing software tool that uses long reads to enhance genome assembly.
GNU General Public License v3.0
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TGS-gapcloser: Aaborted (core dumped) #54

Closed liuxin-21d closed 2 years ago

liuxin-21d commented 2 years ago

Hi Dear Developer, I first used ont long reads to fill gaps. In most cases, it works well, but sometimes, it was aborted by accident.
When i used hifi reads to fill gaps, it always was killed by system. ERRORS like: 截屏2022-09-28 22 10 03

截屏2022-09-28 22 13 12

always being aborted in filling gaps: 截屏2022-09-28 22 14 32

what should i do to avoid being aborted (core dumped), Any help would be appreciated!

Xin Liu

cchd0001 commented 2 years ago

Hi Xin Liu,

Thanks for your interest in this project. Could you please provide more details of the file hifill.fill.log?

Normally, the "std::bad_alloc" error means that the process requires more memory than you provided. Please check #49 and #42 for more details.

Best wishes Lidong Guo

liuxin-21d commented 2 years ago

Hi Lidong,

Thank you for your reply. Here are the hifill.fill.log. 截屏2022-09-29 09 28 13

Xin Liu

cchd0001 commented 2 years ago

Please check https://github.com/BGI-Qingdao/TGS-GapCloser/issues/49 and https://github.com/BGI-Qingdao/TGS-GapCloser/issues/42 for more details