I have a dds object such like:

> dds   
class: DESeqDataSet 
dim: 49305 1091
metadata(2): data_release version
...     

And when I run the DESeq(), it was stuck on the step of "gene-wise dispersion estimates". I have tried both "locol" and "mean" for fitType and it didn't help. I terminated it by running about 1 hr.

> dds<-DESeq(dds, fitType="mean")
   estimating size factors 
   estimating dispersions
   gene-wise dispersion estimates

I’ve recommended here and elsewhere to use limma-voom when you have hundreds of sample size per group, as it’s much faster than solving a GLM, which involves iteration for each gene.