conceptual justification of dada2 truncation prior to merging

[Nicholas_Bokulich]

@Peter_Kos

I have had a thread here in the Forum related to this issue. My resources were not at all used up and still dada2 threw an error, for which eventually some of your colleague said that (1) I should run then dada2 on 18 threads, and (2) perhaps some R geeks could be able to fish out the cause.

For reference, here is the topic you are referencing:

Error with multithreaded dada2 [Plugin error from dada2. An error was encountered while running DADA2 in R (return code 1)]

The issue is not that you are requesting more threads than are available. It is that each thread you request will increase the cumulative memory load until it goes over the top. This is described on the dada2 issue tracker. dada2 often takes a good chunk of memory to run on a single thread — it is very difficult to predict how much memory a single run would use but memory issues with a single thread are common enough (just look around this forum for examples). If you set threads=0 (to use all …

So this boils down to memory limitations that you would encounter one way or another with dada2, and this is not specific to running dada2 in QIIME 2.