search

ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
Other
763 stars 138 forks source link

== Error == system call for: "['spades-core', 'K55/configs/config.info']" finished abnormally, OS return value: -7 #1363

Open dozhun opened 2 months ago

dozhun commented 2 months ago

Description of bug

Hi everyone, I encountered an error while using SPAdes-3.15.5 to assemble a diploid genome (~560 Mb) with 0.67% heterozygosity. About 124 GB of corrected reads were provideed to the assembler. Is there anything that can be adjusted to achieve a complete assembly?

spades.log

spades.log

params.txt

~/biosoft/SPAdes-3.15.5-Linux/bin/spades.py --cov-cutoff 5 --isolate -t 32 -m 1200 -1 N199_spades/corrected/N199_1.clean.fq.00.0_0.cor.fastq.gz -2 N199_spades/corrected/N199_2.clean.fq.00.0_0.cor.fastq.gz -o N199_spades_5

SPAdes version

SPAdes-3.15.5

Operating System

CentOS Linux 7 (Core)

Python Version

Python 3.10.8

Method of SPAdes installation

binaries

No errors reported in spades.log

asl commented 2 months ago

Hello

It might happen that you ran out RAM. Can you give SPAdes 4.0 a try?