spades-core: /opt/conda/conda-bld/spades_1664217775513/work/src/project/spades/main.cpp:101: int main(int, char**): Assertion `cfg::get().K >= runtime_k::MIN_K && cfg::get().K < runtime_k::MAX_K' failed.finished abnormally, OS return value: -6

ablab / spades

SPAdes Genome Assembler

http://ablab.github.io/spades/

Other

713 stars 131 forks source link

spades-core: /opt/conda/conda-bld/spades_1664217775513/work/src/project/spades/main.cpp:101: int main(int, char**): Assertion `cfg::get().K >= runtime_k::MIN_K && cfg::get().K < runtime_k::MAX_K' failed.finished abnormally, OS return value: -6 #1284

Open GuillaumeDore11 opened 2 months ago

GuillaumeDore11 commented 2 months ago

Description of bug

OS return value: -6 after the use of K149 but it's working for K55.

spades.log

params.txt

SPAdes version

SPAdes 3.15.

Operating System

Linux-3.10.0-1160.76.1.el7.x86_64-x86_64-with-glibc2.17

Python Version

Python 3.12.3

Method of SPAdes installation

conda

No errors reported in spades.log

[X] Yes

andrewprzh commented 2 months ago

Dear @GuillaumeDore11

This looks quite odd, since 127 is the maximal possible value and there are multiple checks for that. Is it possible you SPAdes version was modified by someone?

Meanwhile, I suggest setting K-mer size manually -k 55,127.

Best Andrey

GuillaumeDore11 commented 2 months ago

Hi @andrewprzh, Thanks for the answer. I thought that the kmer size limit had been increased in a latest update. If that's not the case I don't quite understand why it has been able to set a value > 127. I just installed with conda and didn't modified it. Guess, I will use -k 55, 127. Thanks again.