Hi @Joely_Corrales,
The sneaky reason this is failing is this line:
5: stop("attempt to make a table with >= 2^31 elements")
R has a limit to the amount of elements in a table and you are hitting the max.
This indicates that you have a lot of unique sequences in your data. This could pretty easily happen if you are not using amplicon sequences and instead using metagenomic shotgun sequences, where, instead of having a target region, the sequences are stochastically random. If that's the case, I'll point you to our metagenomic documents. Whole metagenome analysis with MOSHPIT - MOSHPIT documentation
if not, here is an individual running into the same issue with amplicon data and they reported their process: DADA2 execution halted (Error in table: attempt to make a table with >= 2^31 elements) - #6 by potatoo