finished abnormally, OS return value: -6 None

ZainBioBytes commented 11 hours ago

Description of bug

I am running many samples all together for the assembly, almost all others are finished with spades assembly process. However, few samples are giving some error:

== Error == system call for: "['/shared/homes/25180175/mambaforge/envs/metaenv/bin/spades-core', '/K101/configs/config.info', '/K101/configs/mda_mode.info', '/K101/configs/meta_mode.info']" finished abnormally, OS return value: -6 None

spades.log

log and params.zip

params.txt

log and params.zip

SPAdes version

4.0.0

Operating System

Windows 11 (VS code)

Python Version

3.11.9

Method of SPAdes installation

conda

No errors reported in spades.log

[X] Yes

asl commented 11 hours ago

The log clearly reads:

mimalloc: error: unable to allocate OS memory (17184063488 bytes, error code: 12 [Cannot allocate memory], address: (nil), large only: 0, allow large: 1)
mimalloc: process info:
   elapsed:   18993.877 s
   process: user: 443327.951 s, system: 1509.456 s, faults: 498002
       rss: current: 183624851456, peak: 204591001600
    commit: current: 183624851456, peak: 216846753792

So you are running out of RAM

ZainBioBytes commented 10 hours ago

Thank you! A quick question: I’m currently allocating "-m 235" to SPAdes and 240 to the PBS script. Should I increase both, or would it be better to keep "-m 235" for SPAdes and only increase the PBS memory allocation?

asl commented 10 hours ago

Per SPAdes manual (https://ablab.github.io/spades/running.html#advanced-options):

-m (or --memory ) Set memory limit in Gb. SPAdes terminates if it reaches this limit.

ablab / spades