spades == Error == finished abnormally, OS return value: -9

[CS-CH]

Hi,

Here is an error after I ran Unicycler. It seems like a bug of spades. Is there any way to solve this problem? Thank you.

== Error == system call for: "['./SPAdes-3.15.4-Linux/bin/spades-core', './spades_assembly/K27/configs/config.info', './spades_assembly/K27/configs/isolate_mode.info']" finished abnormally, OS return value: -9 None

======= SPAdes pipeline finished abnormally and WITH WARNINGS!

=== Error correction and assembling warnings:

• 0:20:10.396 7562M / 13G WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 2
• 0:20:10.401 7562M / 13G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 2 ======= Warnings saved to ./spades_assembly/warnings.log

[parul-sharma]

I have the same issue. I am trying to run hybrid assembly and the run throws an error at the first iteration of spades (k27) and exits.

Here's my SPAdes dependency check:

System information: SPAdes version: 3.15.5 Python version: 3.9.16 OS: Linux-3.10.0-1062.18.1.el7.x86_64-x86_64-with-glibc2.17

And here's the Unicycler dependency check:

Dependencies: Program Version Status spades.py 3.15.5 good racon 1.5.0 good makeblastdb 2.5.0+ good tblastn 2.5.0+ good

Unicycler version: v0.5.0.

@CS-CH Did you figure out how to resolve this? Any help would be much appreciated!

[pwkooij]

@parul-sharma I had the same problem, but I noticed my SWAP was all full. I resized my SWAP from 2Gb to 8Gb and it seems to be running smoothly now (it's working on the k119 right now and keeps going).

Not sure if you are still trying to get this to work, but this might resolve your problem as well