The unclassified folder within the fastq_pass folder is a group of fastq files that compose of reads which the software was unable to assign to a barcode. The potential cause of this could be that the barcode was either missing from the read as it was not attached during the library preparation, or that the barcode could not be properly read, potentially due to mutations in the barcode sequence (MinKnow should recognize a barcode as long as 60% of the sequence fits the expectation). It is normal to have an unclassified folder as there might always be some reads that cannot be assigned to a barcode due to above mentioned reasons.