pcg did not converge - Githubissues

weizhouUMICH / SAIGE

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pcg did not converge #394

Closed ytao0210 closed 2 years ago

ytao0210 commented 2 years ago

When I used saige to run the step1, an error occurred: "pcg did not converge. You may increase maxiter number. iter from getPCG1ofSigmaAndVector 500" how can i solve this problem?

weizhouUMICH commented 2 years ago

This is usually because the GRM is close to singular and non-invertible. Can you check if there are twins or duplicated samples in the data set?

weizhouUMICH commented 2 years ago

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