search

weizhouUMICH / SAIGE

GNU Lesser General Public License v3.0
188 stars 73 forks source link

error when running X chromosome #326

Closed xchangchop closed 3 years ago

xchangchop commented 3 years ago

Hi Wei, I got an error when running X chromosome. I did get the result for the first 4079 markers, but got the following errors when running the 4080th markers. I also tested a subset of X chromosome, and got the similar issue that I can run through some markers, but can not get the full result.

numPassMarker: 4079 [1] 3227655 Error in if (out.score["pval.noadj"] > 0.05) { : missing value where TRUE/FALSE needed Calls: SPAGMMATtest -> scoreTest_SAIGE_binaryTrait_cond_sparseSigma Execution halted

weizhouUMICH commented 3 years ago

Hi @xchangchop, I think this problem has been fixed in the newer version. Can you please try it?

Thanks, Wei

xchangchop commented 3 years ago

Thank you Wei. I installed the R-SAIGE on bioconda following the instructions from matuskosut (https://github.com/weizhouUMICH/SAIGE/issues/272). I did update saige to the latest version using "conda update r-saige".

matuskosut commented 3 years ago

Hi @xchangchop ,

you should try to update, I recently published the updated version on conda to 0.44.2 https://anaconda.org/bioconda/r-saige/files

xchangchop commented 3 years ago

Thank you both! Works this time.