DADA2 Error: An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more

Technical Support
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Hi there,

Welcome to the :qiime2: forum!

The (most) interesting part of your error message is:

I looked for that error in the forum and I found some posts.

Click for links
  1. Q2-dada2: Error in isBimeraDenovoTable(unqs[[i]], ..., verbose = verbose) : Input must be a valid sequence table
  2. running dada2,error:Error in isBimeraDenovoTable(unqs[[i]], ..., verbose = verbose) : Input must be a valid sequence table.
  3. Error in isBimeraDenovoTable(unqs[[i]], ..., verbose = verbose) : Input must be a valid sequence table.
  4. DADA2 fails to run due to 'Error in isBimeraDenovoTable'

All of them agree the problem is that DADA2 is not merging your paired end reads so you end up with an empty table prior to the chimera removal step. They say that the problem here could be one of the following:

  1. Your forward and reverse reads could be the same. Looking at your demux.qzv I don't think this is the problem¹, but just in case: how did you import your sequences? Via manifest file? Could you check you didn't put forward paths in the reverse paths column?
  2. Your truncation parameters could be too aggressive for paired ends to overlap. I'm also skeptical about this one because 140 looks sensible to me. What is your expected amplicon size?

Cheers,

Sergio

--

¹ Anyway, the shape of the plots looks somewhat strange to me. I don't have enough experience to tell what is going on there but they look different from the typical plot shape.

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