killed by the cgroup out-of-memory handler

[zhachengwan]

Hi! My memory is not fully utilized, why does this problem occur? I have run it several times, and this problem persists. Moreover, the error is only on chromosome 15. Even the longest chromosome, chromosome 1, has produced results. Any idea or suggestion is appreciated.

[hannespetur]

Hey,

You could try to let graphtyper fewer files at a time by setting --max_files_open=N.

Perhaps start with N=100 or half the number of samples you have (which is lower), and then go try to go even lower if it still keeps getting killed.

Best, Hannes