# Why does the GATE pipeline fail with no obvious reason

In case your GATE pipeline fails with an error message similar to "missing value where TRUE/FALSE needed" the job has crashed while executing an R script. You can confirm this by checking the messages surrounding the error. They should contain hints to "package"s and may even be linked to a particular R package called Rcpp.

While this error cannot be sufficiently explained it can be avoided by reducing and/or changing your covariates, in particular the principal components (PCs) in your phenotype-covariate file. This trial-and-error approach is admittedly somewhat cumbersome but has proved successful as removing a small number of PCs prevents convergence from failing but should not dramatically affect the statistics.

When editing your phenotype-covariate file do not forget to modify your json file accordingly, changing the value informing on the used covariates.