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Increase memory allocation for BEDTOOLS_GENOMECOV #344

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SPPearce opened this issue Dec 22, 2023 · 1 comment
Open

Increase memory allocation for BEDTOOLS_GENOMECOV #344

SPPearce opened this issue Dec 22, 2023 · 1 comment
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enhancement New feature or request

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@SPPearce
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Description of feature

The BEDTOOLS_GENOMECOV step can require a lot of memory when working on merged replicates.
In my case (GRCh38), this takes 80-120Gb in total.
The module runs bedtools genomecov, followed by sorting. This sorting step doesn't actually change anything for me, as the bedtools genomecov output is already sorted. I suspect this is always the case, as the input for genomecov must be sorted.
We could also potentially change the tag here, but the tool is not multithreaded so additional cpus are not helpful, and process_high_memory defaults to excessively large amounts of memory.

@SPPearce SPPearce added the enhancement New feature or request label Dec 22, 2023
@SPPearce SPPearce changed the title Increase memory allocation for Increase memory allocation for BEDTOOLS_GENOMECOV Dec 22, 2023
@SPPearce
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Scratch that, I've just tested and hit the following error on a different sample:
CDX18_I_REP3.mLb.clN.bedGraph is not case-sensitive sorted at line 23978872. Please use "sort -k1,1 -k2,2n" with LC_COLLATE=C, or bedSort and try again.
So sorting is required.
Suggest that we just increase the memory allocation for this process, at least when replicates are being merged.

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