Benjamin Callahan

How much memory is available on this machine? Running `assignTaxonomy` with the Silva db is fairly memory intensive, especially the `wSpecies` version.

Try the non `wSpecies` version, and see if that helps. Test it on a small test dataset. In my experience, running Silva on 8GB is not recommended. 16GB seems to...

These are very large amplicon sequencing samples, about 20M reads per sample. Can you clarify that this is expected? What amplicon are you sequencing? Are primers still on the reads?...

Currently on vacation. Will be back next week.

So I think the issue you are running into is just the size of your samples is challenging the computational complexity of the DADA2 algorithm. Roughly, running time for processing...

My first guess is that this would be a memory issue, can you try a quick test where you just run say the first 3 samples, and see if that...

`dada(..., pool="pseudo")` only needs to load one sample into memory at a time, so it's memory usage scales just fine to long reads. But yes, long reads to take more...

The sample names in your otu_table and `sample_data` don't match one another. You can inspect this directly using: ``` otab

Because of the limited information available in short-read 16S, we recommend the more conservative species-level assignmment method (exact, unambiguous matching) implemented in `assignSpecies` for such data. It is still OK...

This isn't the kind of data for which DADA2 is designed, and performance on it would likely range from marginal at best to completely wrong. It sounds like you want...