Error during denoise step

User Support
1

I’m using the following command for the denoise step:

qiime dada2 denoise-paired --i-demultiplexed-seqs demux-subset.qza --o-table table-subset.qza --o-representative-sequences rep-seqs-sub.qza --p-trim-left-f 10 --p-trim-left-r 10 --p-trunc-len-f 150 --p-trunc-len-r 150 --verbose --p-n-threads 28

And I keep getting the following error:

Loading required package: Rcpp
Initial error matrix unspecified. Error rates will be initialized to the maximum possible estimate from this data.
Initial error matrix unspecified. Error rates will be initialized to the maximum possible estimate from this data.
The sequences being tabled vary in length.

I tried updated my dada2, as suggested in a previous post, https://forum.qiime2.org/t/incorrect-version-of-dada2-installed/468?u=linneakh, however, I still get the same error.

Does anyone have any suggestions?

Thanks!

2

Hi @linneakh,

That isn’t an error, that’s standard informational output for that command. Assuming you are getting QIIME 2 Artifacts as output (files ending in .qza, in your case, table-subset.qza and rep-seqs-sub.qza). then everything is working correctly. If not, then the error is probably elsewhere in that output.

3

Oh thanks! I don’t remember seeing those error before, and it seems that the operation proceeded much more quickly this time, so I thought there was a problem I did get a table.qza and rep-seqs.qza output.

4

No problem! dada2 is pretty fast for everything it can do (you can even use the --p-n-threads param to make it faster).

1 Like
5

I don't remember seeing those error before,

You might have been running your previous commands without --verbose, which would hide the output you're seeing.

1 Like
6

Ah, okay. Thanks guys!

7

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