I did upload the data as a fastq file, and used the --type EMPPairedEndSequences option, rather than making a manifest file. The sequencing was a Golay barcoded, multiplexed 2*150nt illumina run using the original EMP primers from Caporaso. Is the --type EMPPairedEndSequences option only for the newer EMP protocol? I'm not sure if qiime2 would make a manifest file upon uploading the data, and if so, how I would access it. Sorry!