Plugin error from DADA2 denoise-paired

[haadas (hadas)]

Hello,
I'll be glad to receive help,
When I try the dada2 denoise-paired plugin:

qiime dada2 denoise-paired --i-demultiplexed-seqs demux-paired-end.qza --o-table table-dada2 --o-representative-sequences rep-seqs-dada2 --p-trim-left-f 9 --p-trim-left-r 9 --p-trunc-len-f 220 --p-trunc-len-r 200 --p-n-threads 40 --o-denoising-stats stats-dada2.qza

I get the following error message:
Plugin error from dada2:
No features remain after denoising. Try adjusting your truncation and trim parameter settings.
Attached the demux file.

demux.qzv (291.5 KB)

Where am I wrong? would appreciate help,

Thanks
Hadas

[Mehrbod_Estaki]

HI @haadas,

Thanks for sharing that file. What is most likely happening is that you are truncating too much off your 3’ ends which is not leaving any overlap in your reads for merging. We can confirm this by visualizing your stats-dada2.qza, though if you can you should update to the 2018.6 qiime2 version which gives better stats on your length distributions.
You’ll need a minimum of 20bp overlap for proper merging so you want to make sure you are not truncating beyond that. If this isn’t possible given your poor reverse reads, you could always just use the forward reads only which are in much better shape. Let us know if you have any questions!