DADA2 denoise-ccs [error message]

[Wei]

Hi, I am recently analyzing the full length 16S rRNA amplicon sequenicng by QIIME2 (version 2023.07). I have encountered an error message during the denosing step.
Below is the commond that I am using for the denonosing:
qiime dada2 denoise-ccs --i-demultiplexed-seqs enrichment-css-demux.qza
--o-table dada2-ccs_table.qza
--o-representative-sequences dada2-ccs_rep.qza
--o-denoising-stats dada2-ccs_stats.qza
--p-min-len 1000 --p-max-len 1600
--p-front AGRGTTYGATYMTGGCTCAG --p-adapter RGYTACCTTGTTACGACTT
--p-n-threads 8
After running this, an error message just pops up:
Plugin error from dada2:
No reads passed the filter. trunc_len (0) may be longer than read lengths, or other arguments (such as max_ee or trunc_q) may be preventing reads from passing the filter.
I wonder whether anyone encountered the same problem and could you please let me know how to fix this?
I attached the sequence quality and sequence number in each sample after importing into QIIME2

Thank you very much for your help!

[lizgehret]

Hi @Wei,

Welcome to the forum!

Your min/max lengths look reasonable (as you're using the recommended values) - it's hard to see the median values from your quality plot, but I'm wondering if there's a possibility that your primer & adapter values are incorrect? These are the main parameters you've included that could discard all of your reads if set incorrectly. If you're certain those are set correctly, could you share your demux file with me to take a closer look at? Thanks!

[Wei]

HI @lizgehret,
Thank you for the reply. You are right and I have consulted the sequencing company and it turned out that they have removed the primers before delivering the data to us. Thank you very much for help~