DADA2:no reads pass the filter

[laoshiren (quliping)]

I have some problems...
I am working with 'qiime dada2 denoise-paired' common. But some of my samples have no reads passed the filter. And maybe the software is stuck..
qiime dada2 denoise-paired
--i-demultiplexed-seqs paired-end-demux.qza
--o-table feature-table.qza
--o-representative-sequences rep-seqs.qza
--o-denoising-stats denoising-stats.qza
--p-trim-left-f 0
--p-trim-left-r 0
--p-trunc-len-f 300
--p-trunc-len-r 230
--verbose
--p-n-threads 16

In fact, the software has been spending a lot of time on this step. The screen output hasn't changed for a long time. Is it still work well? why?

[ebolyen (Evan Bolyen)]

Hi @laoshiren,

It's not unusual for DADA2 to take some time in QIIME 2, but I'm a little concerned about your samples being dropped by the filter.

What is your amplicon, and what (if any) processing was done prior to DADA2?

For example if you were doing ITS, you'd be trimming off the reverse complemented reverse primers on your forward reads and vice-versa, but then you would set a trunc-len of 0 to disable filtering since you don't expect your amplicons to be the same size anyway.