Dereplication pipeline doesn't work

[GiBacci]

Hi,
I have a dataset of 16S sequencing composed by multiple fasta files (54 files) one for each sample. I would like to classify all the sequences in the dataset using the dereplication pipeline in order to speed up the entire process. However when the classification process reaches the end of the analysis, in the hier file there are only the assignments of the dereplicated file and not the assignments of the original files (the 54 files). any help would be appreciated!
Thanks in advance

Giovanni