I have a few of questions about this. I'll get back to you after I get some answers.
To clarify, did you use qiime cutadapt? And out of curiosity, why both cutadapt and Trimmomatic? You probably already know this, but keep in mind that you anything done outside of QIIME won't be accounted for in provenance data.
Good luck! Rumor has it that Devon's classifiers are memory intensive and that the NCBI classifier might be a pinch smaller. Here are some other links that may come in handy:
