If the job is failing for exceeding memory (this message), with this particular tool the failure can sometimes be resolved by swapping the order of the inputs on the tool form. Be aware that this changes the merge logic applied to the data.
There are a few different tools that can be used to merge/join data within Galaxy. Do a tool search on the keyword "join" to see the different options and/or review tools in upper tool groups at http://usegalaxy.org that manipulate/parse data to locate the alternatives.
Some inputs are so large that they will always fail. Breaking the data up and running in batch, then concatenating the results, is sometimes an option. Other times moving to a local or cloud Galaxy with resources that you control is a solution.
Hopefully, this helps! If you are working at http://usegalaxy.org, or can reproduce the problem there, and would like help determining if the error is due to format problems versus data that is truly too large to process, a bug report can be sent in for feedback.
Thanks! Jen, Galaxy team