I am having an issue with the command vsearch cluster-features-de-novo. Here's the workflow: I have multiple runs for a project and want to merge the two runs together for diversity analysis. Both runs were independently run through DADA2 for denoising. A couple of samples were in both runs becau…

Hi there @Heather_E ! [image] Heather_E: Now I want to cluster at 99% because I am getting multiple features for the same species when I assign taxonomy I am not sure if I follow the rationale here. [image] Heather_E: However, if I filter the table How did you filter the feature table…

I exported the original table as a biom, then converted to tsv. Removed duplicate samples and negative controls using an R script, then converted back to biom and imported as qza.

[image] Heather_E: Fatal error: Invalid (zero) abundance annotation in FASTA file header Well, I am not a vsearch developer, but, that error message sounds to me like you have features in your FeatureData[Sequence] that are either not present in your FeatureTable[Frequency], or, if they are t…

That might be it. Especially because the negative samples were effectively brought down to 0 for features in that sample after running the R script. I will try filtering out the zero abundance reads and see what happens. Thank you!

FYI, it worked! Thanks for your help.

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