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ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
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ERROR #1344

Closed xiaobai5456 closed 3 months ago

xiaobai5456 commented 3 months ago

Description of bug

== Error == system call for: "['/home/chn/miniconda3/envs/spades/bin/spades-hammer', '/mnt/e/gene/00.CleanData/G1-E1/output_dir/corrected/configs/config.info']" finished abnormally, OS return value: -6 None

spades.log

spades.log

params.txt

params.txt

SPAdes version

Spades v.4.0.0

Operating System

Linux-5.15.153.1-microsoft-standard-WSL2-x86_64-with-glibc2.31

Python Version

Python version: 3.12.4

Method of SPAdes installation

conda

No errors reported in spades.log

asl commented 3 months ago

The log reads:

mimalloc: error: unable to allocate OS memory (884998144 bytes, error code: 12 [Cannot allocate memory], address: (nil), large only: 0, allow large: 1)

So you are running out of RAM

xiaobai5456 commented 3 months ago

What should I do

asl commented 3 months ago

What should I do

Run you assembly job on machine with more RAM

xiaobai5456 commented 3 months ago

But I installed spades on Ubuntu，Do I need to install spades separately?

asl commented 3 months ago

But I installed spades on Ubuntu，Do I need to install spades separately?

Sorry, I do not follow. Certainly, in order to run SPAdes elsewhere you need to install it there