search

NBISweden / Earth-Biogenome-Project-pilot

Assembly and Annotation workflows for analysing data in the Earth Biogenome Project pilot project.
https://www.earthbiogenome.org/
GNU General Public License v3.0
9 stars 8 forks source link

Out of memory kill issued by slurm but Nextflow process marked as completed. #81

Open mahesh-panchal opened 4 months ago

mahesh-panchal commented 4 months ago

Describe the bug The logs show slurm encountered an error, however the Nextflow process is marked as COMPLETED. No error was raised

.command.log:

INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
INFO:    Environment variable SINGULARITYENV_SNIC_TMP is set, but APPTAINERENV_SNIC_TMP is preferred
slurmstepd: error: Detected 1959 oom_kill events in StepId=45226719.batch. Some of the step tasks have been OOM Killed.

Nextflow log status:

$ nextflow log -f process,tag,status $( nextflow log -q | tail -n 1 ) -F "process == 'ASSEMBLE_HIFI:GFATOOLS_GFA2FA'"
ASSEMBLE_HIFI:GFATOOLS_GFA2FA   hifiasm-raw-default COMPLETED

To Reproduce Not sure how to reproduce.

Expected behavior When an out of memory error occurs, Nextflow should also report the error.

Additional context Add any other context about the problem here.