search

ablab / spades

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

== Error == system call for: spades-core, finished abnormally, OS return value: -9 #1338

Open RJEGR opened 4 months ago

RJEGR commented 4 months ago

Description of bug

Hello,

I have had a great experience using SPAdes for assembly de novo transcriptomes,

Unfortunately, I have trouble running rnaSPAdes now,

It finished abnormally by running the K73 assembly step.

I'm using bulked Paired-end files (~20 Gb per PE file) as follows:

rnaspades.py \
 --checkpoints last \
 --pe1-1 bulk.1.P.qtrim.fq.gz --pe1-2 bulk.2.P.qtrim.fq.gz \
 --pe1-fr -t 24 -m 100 --cov-cutoff auto -o $PWD

The error line tailed in the spades.log is:

10:46:08.165    67G / 110G  INFO    General                 (sequence_mapper_notifier.h:  77)   Processed 134400000 reads

== Error ==  system call for: "['/LUSTRE/apps/bioinformatica/SPAdes-3.15.5-Linux/bin/spades-core', '/LUSTRE/bioinformatica_data/genomica_funcional/rgomez/Nodipecten/02.Assembly/K73/configs/config.info', '/LUSTRE/bioinformatica_data/genomica_funcional/rgomez/Nodipecten/02.Assembly/K73/configs/mda_mode.info', '/LUSTRE/bioinformatica_data/genomica_funcional/rgomez/Nodipecten/02.Assembly/K73/configs/rna_mode.info']" finished abnormally, OS return value: -9

is this an error due to memory exceeding 110 Gb?

Any suggestion?

Best regards

spades.log

spades.log

params.txt

params.txt

SPAdes version

SPAdes genome assembler v3.15.5 [rnaSPAdes mode]

Operating System

Linux 3.10.0-1160.el7.x86_64

Python Version

Python 2.7.5

Method of SPAdes installation

binaries

No errors reported in spades.log

asl commented 4 months ago

Your SPAdes job was killed, likely more information could be found in the system log. You might also want to give SPAdes 4.0 a try