finished abnormally, OS return value: -6

Asraid commented 2 months ago

Description of bug

Hi, I have not been able to run a pair-ends reads metagenome assembly. I changed the memory limit from 31 Gb to 64 but it didn't work. I changed the Python version from 3.11 to 3.8 and nothing. Thanks.

spades.log

spades.log.txt

params.txt

SPAdes version

Spades 4.0.0

Operating System

Ubuntu 22.04.4 LTS

Python Version

Python 3.8.19

Method of SPAdes installation

conda

No errors reported in spades.log

[x] Yes!

asl commented 2 months ago

Please upload your spades.log file and params.txt

Asraid commented 2 months ago

Sorry. I just upload the files. Thanks.

asl commented 2 months ago

The log reads:

mimalloc: error: unable to allocate OS memory (43494932480 bytes, error code: 12 [Cannot allocate memory], address: (nil), large only: 0, allow large: 1)
mimalloc: process info:
   elapsed:     323.887 s
   process: user: 3902.244 s, system: 69.634 s, faults: 40
       rss: current: 67264512, peak: 288595968
    commit: current: 67264512, peak: 434266112

So, you are running out of RAM. Given the size of your dataset I doubt you will be able to assemble it using 31 Gb of RAM. 64 Gb is unlikely to help (though it does not seem you're having that amount of RAM on that machine).

ablab / spades