denoise-ccs- loosing almost 60% of reads at denoising step of dada2

I am processing my pacbio 16S rRNA reads through denoise-ccs and as
stats-dada2.qzv (1.2 MB)
you can see from the table I am losing almost 60% of my reads at the denoising step. Could anyone help me to improve this? I have tried changing the --p-max-ee but that does not help..

dada2 denoise-ccs --i-demultiplexed-seqs demux-single-end.qza
--p-min-len 1000
--p-max-len 1600
--p-n-threads 4
--o-representative-sequences rep-seqs-dada2.qza
--o-table table-dada2.qza
--o-denoising-stats stats-dada2.qza



The go to place to start when you are losing more reads than you expected, is to really double check that all non-biological sequences have been removed from your reads, so that is a good place to start. You also might want to watch these videos from one of our workshops about both the theory of denoising and actually running the tools: Lecture & Plugin Tutorial.

However, in your case, I think it likely due to something we are not aware of yet in regards to how DADA2 processes CCS reads, could you try removing --p-min-len and --p-max-len and see if that helps?