There's not better answer than the one I found posted by amit
The "singularity" error you are getting occurs when your covariates
are confounded with batch (or with each other). In the example you are
trying is there a batch that contains only one covariate level and is
that covariate level exclusive to the batch? If this does not make
sense, post your 'pheno' variable in a reply and I will be happy to
help you figure out the problem.
Got FAQ: What's a reproducible example (`reprex`) and how do I create one?