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ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
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Memory allocation error and abnormal termination, OS return value: -6 #1404

Open vivaxp5 opened 1 month ago

vivaxp5 commented 1 month ago

Description of bug

  1. I am getting an error regarding memory allocation despite having sufficient resources available.
  2. The run terminated abnormally.

spades.log

spades.log

params.txt

params.txt

SPAdes version

SPAdes genome assembler v4.0.0

Operating System

Ubuntu 22.04.5 LTS

Python Version

Python 3.12.2

Method of SPAdes installation

Conda

No errors reported in spades.log

jspychalla commented 2 days ago

Runs for two of my samples terminated in the same way while most of my other samples ran successfully. Did you figure out how to solve this ?

jspychalla commented 2 days ago

Here are my params.txt and spades.log files : params.txt spades.log

asl commented 2 days ago

@vivaxp5 How do you know if the resources are sufficient? It seems you provided 400 Gb of RAM to SPAdes and sadly your assembly requires more, everything stopped when these were exhausted.