Sub.sample multiple filetypes simultaneously

Not sure if this is a feature request or a user error report. I thought that I used to be able to sub.sample the shared and the taxonomy at the same time.

  sub.sample(, count=XC152IBSandHC.trim.contigs.good.unique.good.filter.precluster.denovo.vsearch.pick.pick.count_table, shared=current, list=XC152IBSandHC.trim.contigs.good.unique.good.filter.precluster.pick.pick.opti_mcc.list, size=5000, persample=true, label=0.03)
Sampling 5000 from each group.

Output File Names: 

This runs but only outputs the subsampled shared?