Benjamin Callahan

A couple more things that might help diagnose. First, try to make this a "minimal example" -- does this error also arise when just running a single sample? I.e. if...

That looks normal. I'm not sure what's going on. Another thing to try would be to check if your `filterAndTrim` can process files known to work correctly. Are you able...

I'm not sure. There must be something about those CCS fastq files in particular? Maybe the easiest thing at this point would be if you could share one of the...

benjamin DOT j DOT callahan AT gmail DOT com

So, this code runs fine for me: ``` library(dada2); packageVersion("dada2") fn

> One more question, can it be a matter to use Rstudio? Rstudio can crop up its own bugs at times, but I don't see how it would affect the...

It is hard to diagnose when the error won't replicate on my own machine, and in fact runs fine. As for the 10% of the file working, I doubt this...

Although not true in most cases, chimera removal can become the most computationally costly step in some datasets. There are tools to address this though, and also possible to better...

> The sequencing platform used 4 different primer sequences that vary from 1-3nt. Those extra bases were present before the FWD & REV primers. Hence, I couldn't use trimLeft as...

DADA2 can still work, but the more of those unremoved primers there are, the more issues are going to crop up. My concern is that despite what the `primerHits` function...