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bahlolab / superSTR

A lightweight, alignment-free utility for detecting repeat-containing reads in short-read WGS, WES and RNA-seq data.
GNU General Public License v2.0
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stack smashing detected #21

Closed wdecoster closed 1 year ago

wdecoster commented 1 year ago

Hi,

I realize that this gives you very little information to debug, so please let me know what I can do to gather more information about this error. I installed superSTR using conda (mamba), and I am running this using slurm on BAM files. My jobs end up with a non-zero exit code after a few hours, printing to stderr:

*** stack smashing detected ***: <unknown> terminated
srun: error: mforge157: task 0: Aborted (core dumped)

Do you have an idea of how to solve this?

Wouter

lfearnley commented 1 year ago

Just double checking - strdust or superSTR?

On Tue, 7 Nov 2023, 6:06 am Wouter De Coster, @.***> wrote:

Hi,

I realize that this gives you very little information to debug, so please let me know what I can do to gather more information about this error. I installed strdust using conda (mamba), and I am running this using slurm on BAM files. My jobs end up with a non-zero exit code after a few hours, printing to stderr:

stack smashing detected : terminated srun: error: mforge157: task 0: Aborted (core dumped)

Do you have an idea of how to solve this?

Wouter

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wdecoster commented 1 year ago

Oh. Let me fix that :-D

lfearnley commented 1 year ago

Haha, I know that feeling!

We haven't encountered a stack smash yet and will need to a bit of additional information.

I think the first step for debug will be to build from source with the -g flag, see if it still faults, and if so, try it under valgrind if available using exp-sgcheck.

This should give a stack trace that'll be informative as to where things are going awry.

On Tue, 7 Nov 2023, 6:38 am Wouter De Coster, @.***> wrote:

Oh. Let me fix that :-D

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wdecoster commented 1 year ago

I think the first step for debug will be to build from source with the -g flag, see if it still faults

That already solved the problem :)