pairtools sort not parallelizing

[SooLee]

It may be related to this issue: https://superuser.com/questions/938558/sort-parallel-isnt-parallelizing

[agalitsyna]

Hi, thanks for reporting this. Can you provide more details on the observed behavior and elaborate on what was expected?

[agalitsyna]

The solution provided in the SO link above (i.e. setting the buffer size manually to 1G or bigger) is already implemented via the --memory flag of pairtools sort. To debug this issue further we would need a reproducible example.