minimap2 self mapping step use so much memory, it is unbelievable!

[xiekunwhy]

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.

Best,
Kun

[ShunOuchi]

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

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