in reply to Re: Out of Memory when generating large matrix
in thread Out of Memory when generating large matrix

Hi! Thank you so much for your reply! So the goal I try to achieve here is that as for the 21mer I'm working on, it is a sequence of 21 letters, each position can have 4 variable "AGCT". Therefore, in total, it should have 4**21 combination. I have total 197 kmer files, each of them contains around 8000 of these 21mers, and I'm trying to count how many time each 21mers has shown among these 197 files. That's why I need a matrix to do so.

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Re^3: Out of Memory when generating large matrix
by BrowserUk (Patriarch) on Mar 05, 2018 at 16:39 UTC
    Therefore, in total, it should have 4**21 combination.

    Yes. But not all of them -- in fact a very small percentage -- will appear; so rather than reserving space for trillions of counts that will 99% never be used, you can choose to only count those that do appear. That will save huge amounts of space and speed up your processing.

    With 197 files * 8000 lines, there are at most 1.5 million 21kmers -- if they are all unique -- so there in no need to reserve space for all 4.3 trillion possibilities. 197*8000 / 4.3e12 * 100 = 0.0000358%

    I'm trying to count how many time each 21mers has shown among these 197 files.That's why I need a matrix to do so.

    Fair enough, but you don't need to count them all in one huge matrix. You can process the 197 files one by one and only store the nonzero counts across files.

    Could you post a small sample (say 20 lines) of what is in your kmer files?

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Re^3: Out of Memory when generating large matrix
by hippo (Archbishop) on Mar 05, 2018 at 16:45 UTC

    197 * 8000 = 1576000. If you only have 1.5e6 data points why are you trying to match them against 4**21 possible combinations when all bar an infinitessimal fraction of those won't be present?

    Just compare your 1.5e6 against themselves and mark everything else as zero. No matrices required.

    For fun, see The 10**21 Problem (Part I) and the subsequent parts.

    (Edit: BrowserUk managed to construct a fuller and therefore better response in the time it took me to deduce and type this. Still, great minds and all that ;-)

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