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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In reply to Re^3: Out of Memory when generating large matrix by BrowserUk
in thread Out of Memory when generating large matrix by cathyyihao

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