Dada2 or Deblur

[Achraf_Zbaida (Achraf Zbaïda)]

I want to use DADA2 or Deblur to generate FeatureData[Sequence] and FeatureTable[Frequency] , but both commands are not working.

DADA2 :

qiime dada2 denoise-single
--i-demultiplexed-seqs demux.qza
--p-trim-left 0 --p-trunc-len 0
--o-representative-sequences rep-seqs.qza
--o-table table.qza
--o-denoising-stats denoising-stats.qza
--p-n-threads 0

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.

DEBLUR:

qiime deblur denoise-16S
--i-demultiplexed-seqs demux.qza
--p-trim-length -1
--o-representative-sequences rep-seqs.qza
--o-table table.qza
--p-sample-stats
--o-stats deblur-stats.qza
--p-jobs-to-start 16

Plugin error from deblur:

No sequences passed the filter. It is possible the trim_length (-1) may exceed the longest sequence, that all of the sequences are artifacts like PhiX or adapter, or that the positive reference used is not representative of the data being denoised.

[Oddant1 (Anthony Simard)]

Hello @Achraf_Zbaida, it is unclear to me why none of your sequences are passing the filter, can you please DM me your demux.qza? Thank you.

[Oddant1 (Anthony Simard)]

Can you try running qiime dada2 denoise-single with --p-trunc-len 70? That should cut off that weird bit where the scores dip, but I'm not sure how much that will matter. If that doesn't work then can you please upload your file to Megaupload or Dropbox or similar and DM me a link to the file? There is potentially something strange going on with your demux.qza, the scores aren't usually so flat.