terminate called after throwing an instance of 'std::bad_alloc'

[ERA]

Hi everyone,

My process to generate genome indexes using STAR is aborted probably because of a memory issue.

terminate called after throwing an instance of 'std::bad_alloc'

  what():  std::bad_alloc

Aborted

I’d like to send my Log.out file but it has too many rows (7189346 rows). I do not know which part of it is necessary to detect the issue.

Any help please?

[ERA]

This issue seems to be fixed when I reduced the value for the --genomeChrBinNbits option from 12 to 8

[Alexander Dobin]

Hi @ERA,

it seems that your genome assembly has a lot of scaffolds, which does indeed require lowering of the --genomeChrBinNbits .

Cheers

Alex