Hi @Harry,
The Deblur algorithm needs the sequences to be the same length. I suspect that specifying --verbose on the run will indicate the issue. Using --p-trim-length 350 will trim your reads to a maximum of 350nt, and anything less than 350nt will be dropped.
Please note that Deblur has not been evaluated with Ion Torrent and its error profiles are based off of Illumina data.
Best,
Daniel