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ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
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spades-core terminated automatically during k-mer counting without errors #1237

Open yqy6611 opened 7 months ago

yqy6611 commented 7 months ago

Description of bug

I tried to assemble metagenome reads via SPAdes (--meta), yet only the first k-mer can be assembled successfully without other manipulations. During the second k-mer assembly, spades-core process disappeared automatically during k-mer counting phase without any error messages.

spades.log

spades.log

params.txt

params.txt

SPAdes version

SPAdes v3.15.5

Operating System

Ubuntu 22.04

Python Version

Python 3.12.1

Method of SPAdes installation

conda or manual

No errors reported in spades.log

asl commented 7 months ago

I would suggest you to ask your system administrator. This looks like some problem at your end, e.g. some i/o problem

yqy6611 commented 7 months ago

This is our own workstation. So any suggestions on how to fix this issue?

asl commented 7 months ago

Check your system log. Might be something there

yqy6611 commented 7 months ago

I have checked the system log, but there are no errors related to this.