How to prune the features using recursive feature elimination?
StratifiedKFold tries to keep balance between representation of classes in each fold. You have 5 folds and one or more of your classes have less than 5 instances in the data i.e. they can not be spread among 5 folds. So you can not use it.
That was the minor problem. ML-wise you have very few data points so the right way to cross-validate is leave-one-out.