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ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
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System call finished abnormally, OS return value: -9 #1053

Open sclipman opened 1 year ago

sclipman commented 1 year ago

Description of bug

Thank you for your work on this incredible software. I have enjoyed SPAdes for many years. I am hoping you can help me resolve an error I'm now receiving when trying to run SPAdes on an HPC cluster to assemble 150 bp metagenomic reads.

== Error == system call for: "['/home/sc/Resources/SPAdes-3.15.5-Linux/bin/spades-core', '/home/sc/XF1620/XF1620/K55/configs/config.info', '/home/sc/XF1620/XF1620/K55/configs/mda_mode.info', '/home/sc/XF1620/XF1620/K55/configs/meta_mode.info']" finished abnormally, OS return value: -9

Please find the log and parameter files attached below.

I appreciate any insight!

spades.log

spades.log

params.txt

params.txt

SPAdes version

SPAdes v3.15.5

Operating System

Linux-4.18.0-147.el8.x86_64-x86_64-with-centos-8.1.1911-Core

Python Version

Python v3.6.8

Method of SPAdes installation

Linux binary

No errors reported in spades.log

ditag commented 1 year ago

Hello,

I would also like to follow this thread as I am facing the exact same problem. Metagenomic reads 2x150bp, System information: SPAdes version: 3.15.5, Python version: 3.9.5, OS: Linux-3.10.0-1160.11.1.el7.x86_64-x86_64-with-glibc2.17

I am using for loop to run my samples - some samples manage to assemble but majority don't..

Thank you in advance for your consideration, Dita

asl commented 1 year ago

@ditag Please open a separate issue as it could be different from the topic starter.

asl commented 1 year ago

@sclipman It looks like you might be running out of RAM. How much free RAM is available for your SPAdes job?

sclipman commented 1 year ago

@asl There is 180 GB of RAM available. I have never had trouble running our samples with this amount of RAM in the past. I tested an older file that successfully assembled back in 2021 but am now receiving an error with this latest version of SPAdes, so I'm not convinced it's due to limited RAM.

ditag commented 1 year ago

@asl I also received "OS return value: -9".

After previous recommendation on increasing the RAM, I re-run my samples with 24 procs and 240GB, and so far seems that it worked.