ChIPQC : ChIPQCreport(experiment) swap memory overload
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ZheFrench ▴ 20
@zhefrench-11689
Last seen 8 days ago
France

Hey,

I'm trying to generate a ChIPQCreport on my 21 samples described in my sample sheet for all chromosomes .

Memory use is increasing too fast, using all free memory and then it's going to swap memory which is also limited and then overload swap so the creation of the report will crash.

Is there a way to tell ChIPQC to use a directory on disk to write stuffs instead of using swap...or to tell don't use so much memory or so much cores...

Note that swap memory is not released after the crash and even when you kill R.

By the way,  I'm working on a system with 64GB and 32 cores. 

Linux  3.16.0-4-amd64 #1 SMP Debian 3.16.39-1 (2016-12-30) x86_64 GNU/Linux

R Version Information

  • Version: 3.3.1

  • Version_String :R version 3.3.1 (2016-06-21)

ChIPQC Version Information

  • Version: ChIPQC:1.10.3

 

 

 

ChIPQC ChIPQCreport • 743 views
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@thomas-carroll-7019
Last seen 16 months ago
United States/New York/The Rockefeller …

 

Hi, it may have been that some of bigger files running in parallel were  causing it to run out memory.

Lowering the number of core will often solve this.

Best

Tom

 

 

 

 

 

 

 

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Entering edit mode
ZheFrench ▴ 20
@zhefrench-11689
Last seen 8 days ago
France

Ok playing with register from BioCparallel by limiting the number of cores , you limit memory usage , it should make the trick. But anyway, it's buggy.

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