Hello Javad,
for IonTorrent sequences with barcodes in the sequences it is recommended to use "qiime cutadapt demux-single". Therefore you have to modified your column BarcodeSequence. Before every barcode you have to add on ^ sign e.g ^CTAAGGTAAC otherwise cutadapt will not work properly. More information see:
(Problem with cutadapt demultiplexing of IonTorrent data - #9 by Stratering)
The linker sequence will be removed anyway because the recommendation of dada2 for IonTorrent is to cut the first 15bp but you can also use "qiime cutadapt trim-single" to remove the Linker and the Primer.
Hope it helps.