[galaxy-user] Join, Subtract and Group PLUS large GOA files

Hello all, I've been using the "Join, Subtract and Group" to join my transcriptome/annotation data to GO and GO Slim for some time (in the Main galaxy). I just updated my GO files as I've run a a new data set, and have been having trouble with the joining function, it never seems to complete (while before it would be done in just a few minutes). It works just fine joining my "new data" with my "old" GO files (which of course are now out of date) but not the new GO files from both my collaborator and from EBI (specifically the unipro). Not sure if its a file size limitation? Thanks, Colleen