Closed shimaomao26 closed 2 years ago
hi, I met the same problem with you, but my task is not done yet. I ran SAIGE in 100k samples for binary traits with 32 threads in step1, but 24 hours have passed, and the task has not been completed, how long did it take you to run 100k individuals?
hi, I met the same problem with you, but my task is not done yet. I ran SAIGE in 100k samples for binary traits with 32 threads in step1, but 24 hours have passed, and the task has not been completed, how long did it take you to run 100k individuals?
Hi, in my case it's 1.5 days on 32 threads.
Thank you! My task has finished today, which used 34hours with 32 threads.
Hi @ytao0210 and @shimaomao26,
Thanks for reporting the issue! The converging time depends on several factors and may vary by phenotypes. The computation time generally is linear to the number of markers for GRM and slightly more than linear to the number of samples. PCG can failed to converge when GRM is singular. Can you please if there are twins and duplicated samples in your data?
Thanks, Wei
Dear Wei,
Thank you very much for the answer.
In my case the arrayed genotypes were plenty QCed before step1, and would not have the fully related samples. Besides, I tried to run SAIGE 0.38 (without LOCO) on the same (plink) data, but didn't see this warning anymore...
Best Maomao
v0.38, no LOCO
....
user system elapsed
81124.356 508.219 3877.540
t_end - t_begin, fitting the NULL model took
user system elapsed
81063.622 381.378 3864.258
Start estimating variance ratios
v0.44, adding LOCO
...
t_end_Get_Coef_LOCO - t_begin_Get_Coef_LOCO
user system elapsed
21441.274 45.086 2687.342
pcg did not converge. You may increase maxiter number.
iter from getPCG1ofSigmaAndVector 500
t1_Rinv_1 is 6.21698e+15
Nglmm 5.53254e+15
user system elapsed
514686.177 1835.546 65103.890
t_end - t_begin, fitting the NULL model took
user system elapsed
514639.806 1794.683 65081.518
Start estimating variance ratios
Hi @shimaomao26
We have just released a new version 1.0.0. It has computational efficiency improvements for both Step 1 and Step 2 for single-variant and set-based tests. We have created a new program github page https://github.com/saigegit/SAIGE with the documentation provided https://saigegit.github.io/SAIGE-doc/
The program will be maintained by multiple SAIGE developers there. Please feel free to try the version 1.0.0 and report issues if any.
Thanks! Wei
Hello,
I am running SAIGE in 100k individuals for binary traits. Every time I could find
pcg did not converge
in the log but the program did neither stop nor raise waring. In the paper it was said that in UKB it took < 10 iters to converge (Supplementary,Figure 12). Interestingly, the step2 result was good in my run, without obvious inflation, and showed high consistence with other Tools.Does it matter? Should I make sure step1 pcg is converged?
Thank you very much!
Maomao
A piece of log: