These are chat archives for nextflow-io/nextflow

4th
May 2019
Stephen Kelly
@stevekm
May 04 01:51
If you do not see .exitcode then I think it means that the .command.run script is not finished, which would suggest that somehow the entire process is being killed. As far as I am aware Nextflow only knows about out of memory errors if there is an explicit error message returned.
To be clear, the OOM Killer I am referring to is a process that runs within Linux and kills other processes based on its own determination of overall system memory availability, so this could kick in without your program ever giving an explicit error. https://www.kernel.org/doc/gorman/html/understand/understand016.html
We've been having a tough time with it especially since we now have cgroups on our system which gives strict limits to the resources a user process can use
Somewhere on the system you can find OOM Killer logs, I might start there and look for entries around the timestamp of the list
Lost process*