Bedtools subtract not dealing well with large datasets
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6.9 years ago
roll ▴ 330

I am using bedtools subtract with large datasets and it keeps crashing, giving the following error

    terminate called after throwing an instance of 'std::bad_alloc'

Is there a way to get over this problem in bedtools?

 

Alternatively is there any other way to find nonoverlapping regions for two bed files?

thanks

bedtools software error • 2.0k views
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Entering edit mode

Watch the process in another terminal window with "top". std::bad_alloc sounds like a memory error, maybe it used all of your memory then ran out? Pre-sorting both lists might help.

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Entering edit mode
6.9 years ago
roll ▴ 330

bedtools intersect -v

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