Issue with DEG analysis with the differential expression tools


I would like to perform an analysis with Deseq2
The data has 3 replicate, but pooled into one dataset. Since the deseq2 need at least 2 dota for each factor, i cant do my analysis now. Is there any options in this tool or any other tools like edgeR or limma.
It is the last step of my analysis which get 3 months of my time. Really need some help right now.