vdemichev / DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.
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Out of memory for DIA phospho dataset #753

Closed rolivella closed 1 year ago

rolivella commented 1 year ago

Hello, we're trying to run DIANN for a phosphoproteome with 30 raw files with this additional config params:

--var-mods 2
--var-mod UniMod:21,79.966331,STY
--no-norm

At the moment I tested DIANN allocating 64GB but failed.

Do you know how mem should be allocated in order to run this job? Thanks!

vdemichev commented 1 year ago

How does the log look like and how much RAM do you have in the system?

Vadim

rolivella commented 1 year ago

This is the log: rsDIANNsubmission.output.log.zip

I send this job to a cluster queue where I allocated 64GB of mem. After some hours running, the scheduler automatically killed the job: cgroup/OOM: Killed because of memory limit

vdemichev commented 1 year ago

Two comments:

vdemichev commented 1 year ago

Also, can maybe monitor the RAM consumption of the DIA-NN process. DIA-NN itself did not issue a warning, apparently it did not detect potential out of memory event.

rolivella commented 1 year ago

@vdemichev at the end we found a misconfiguration of the mass accuracy that caused the out of memory, as you suggested. I close the issue. Thank you!