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weizhouUMICH / SAIGE

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SAIGE single variant error for allocate large memory #378

Closed ypnngaa-py closed 2 years ago

ypnngaa-py commented 2 years ago

Hi, I am using SAIGE to analyze UKB WES data. Sample size is about 180K after filtering. To reduce the burden, the plink file for null model only contains common variants (MAF>0.01) So far I have no luck running the null model as it failed to allocate large size of memory. 200G mem is close to the limit of the cluster I have access to. Let me know if this is expected and if there is a workaround.

Look forward to hearing from you. Thanks!

See below for the running log error message:

178604 samples have non-missing phenotypes 21027 samples in geno file do not have phenotypes 178604 samples will be used for analysis qr transformation has been performed on covariates Error: cannot allocate vector of size 177.9 Gb Execution halted Warning message: system call failed: Cannot allocate memory

weizhouUMICH commented 2 years ago

Sorry for my late reply.

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