large samples

[hanajori]

Hi

I am trying to PCA with smartpca for 200K sample , 100K SNPS with 256G memory .
However, the process does not finish (core dumped). I suspect memory shortage, but I do not have access to additional memories.

Is this problem is reasonable(compared with memory size)? and Are there any way to solve it?

Thanks,

Satoshi

[Christopher Chang]

You should use the 'fastmode' from EIGENSOFT 6 or later (or equivalently, plink 2.0's "--pca approx" function); that approximation algorithm is simultaneously faster and more memory-efficient in this case.

[hanajori]

Thanks! But I already tried fastmode. I got the result using small samples (like with "poplistname" option), however, using all samples it does not work.

Is it impossible to?

[Christopher Chang]

You have enough memory for the job; maybe you've hit an EIGENSOFT fastmode bug. Try plink 2.0 "--pca approx" then.

[hanajori]

Thank you great advice!
I'll try plink2!