Is it possible to have only one plate of samples in a sequencing run?

Yes. In this case, the 6 nucleotide Illumina small RNA TruSeq i7 index, which identifies the plate, should not be read. Either do not perform an indexing read or use the “--use-bases-mask” option to ignore the 6nt index read.  This should result in a single set of FASTQs for the whole sequencing run. See the demux guide for more information.

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