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ShunOuchi / GreenHill

De novo chromosome-level scaffolding and phasing tool using Hi-C
GNU General Public License v3.0
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minimap2 self mapping step use so much memory, it is unbelievable! #19

Closed xiekunwhy closed 10 months ago

xiekunwhy commented 1 year ago

Hi,

For a 750 M genome, minimap2 self mapping step cost ~600G RAM, how greenhill make minimap2 so worse? unbelievable I think. And minimap2 use only 10 threads even -t 40. image

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Best, Kun

ShunOuchi commented 1 year ago

Hi Kun,

Greenhill only uses minimap2 for self-alignment (-D --secondary=no) and long read mapping, and does nothing special. Therefore, we do not know the cause. Please ask at minimap2 issues.

Thank you, Shun

github-actions[bot] commented 10 months ago

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