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ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
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Cannot allocate memory. Error code: 12 #1279

Closed ucassee closed 2 months ago

ucassee commented 2 months ago

Description of bug

Hi, I meet the following error, how should I fix it? Thanks

== Error == system call for: "['/Share/user/zhou/software/SPAdes-3.15.5-Linux/bin/spades-hammer', '/Share/sediment/02.assemble/00_metaspades/P22B56A/corrected/configs/config.info']" finished abnormally, OS return value: 12 None

spades.log

spades.log

params.txt

params.txt

SPAdes version

3.15.5

Operating System

Linux-3.10.0-1160.el7.x86_64-x86_64-with-centos-7.9.2009-Core

Python Version

python 2.7.5

Method of SPAdes installation

binaries

No errors reported in spades.log

asl commented 2 months ago

Log reads:

 31:58:29.810   325G / 404G  ERROR   General                 (mmapped_reader.hpp        :  52)   mmap(2) failed. Reason: Cannot allocate memory. Error code: 12

So you are running out of RAM. If there is free RAM, then it might be possible that your server is improperly configured and it cannot allocate more than certainly amount to a single process (SPAdes). See https://github.com/ablab/spades/issues/871#issuecomment-965639427 for some suggestions here.