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ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
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OS return value: -6 #1290

Closed Nishofei closed 1 month ago

Nishofei commented 1 month ago

Description of bug

Dear SPAdes team, I'd like to use a mix of second- and third-generation sequencing data. However: == Error == system call for: "['/home/sdae/Barley2/SPAdes-3.15.5-Linux/bin/spades-core', '/home/sdaf/Barley_data/THREE/target_pacbio_1/K55/configs/config.info']" finished abnormally, OS return value: -6 Do you have any suggestions to fix it? Thank you in advance.

spades.log

spades.log

params.txt

params.txt

SPAdes version

3.15.5

Operating System

Linux-5.4.0-150-generic-x86_64-with-debian-buster-sid

Python Version

3.7.6

Method of SPAdes installation

binaries

No errors reported in spades.log

asl commented 1 month ago

For the record, the log reads:

mimalloc: error: unable to allocate OS memory (4194304 bytes, error code: 12 [Cannot allocate memory], address: (nil), large only: 0, allow large: 1)
mimalloc: process info:
   elapsed:   33574.535 s
   process: user: 968031.745 s, system: 5951.798 s, faults: 56
       rss: current: 643874893824, peak: 641814200320
    commit: current: 643874893824, peak: 643879088128

So the problem is quite clear.