I'm using QIIME2 version 2018.2 to perform bacterial community analysis.
All went well and I got the qzv file after denoising and QC filtering ( file attached). However, when i try to do the filtering, merging and removal of quimeras with DADA2, all reads are removed (sudo docker run -t -i -v $(pwd):/data -w /data Quay qiime dada2 denoise-paired --i-demultiplexed-seqs cutadapt_adapters/trimmed_sequences.qza --p-trunc-len-f 0 --p-trunc-len-r 0 --p-max-ee 2 --p-n-threads 4 --o-representative-sequences seqs-dada2.qza --o-table table-dada2.qza --verbose > stdout-dada2.txt)
I tried changing the parameters - increased number of errors, select trunc at 240 and 200, but it still happens.
I installed the newest version of Qiime, however, and even following the pipeline when i get to the filtering and merging point I still loose all the sequences.
Can you post a screenshot of the length distribution tables in the demux visualizer? It might be the case that the your truncation position parameter is causing all reads to be removed.
These are the sequence count distributions. On the page with the per-base quality box plots, at the bottom there should be two tables that give a summary of the distributions of lengths of the reads. I forgot that you already attached your demux visualizer, so I checked that and strangely these tables weren't there at all. Then I checked your provenance and it looks like you're using a 2018.2 release of qiime2. These length distribution tables were added 4 months later it turns out. I recommend updating your version of qiime2 if possible. This will let us see these tables and will also let you run a version of dada2 that has 8+ years of updates.
