Dada2: qiime2 virtual machine vs RStudio performance

User Support
,
3

Hi @Jaroslaw_Grzadziel! There are a number of factors that could be contributing to the differences in performance you’re seeing:

  • You’re running QIIME 2 in a VM, so that will slow things down quite a bit over running the analyses in a native environment (that’s a general drawback of using VMs). You might try checking that the guest operating system has enough RAM and CPU allocated, but things will still be quite slower than a native installation.

  • In the 2017.12 release of QIIME 2, some performance enhancements were made, but the version of DADA2 available in QIIME 2 is still 2x-10x slower than running DADA2 directly from R or RStudio (see these issues for details: 1, 2).

Here are a couple of ideas to speed things up:

  • Run QIIME 2 in a native installation on Linux or macOS (i.e. not in a VM). If that’s not an option, you could use the QIIME 2 Docker image to run QIIME 2 on Windows with minimal performance overhead.

  • Use the --p-n-threads option with the qiime dada2 denoise-* methods to run things in parallel.

  • Use DADA2 from within R or RStudio (i.e. outside of QIIME 2), save the results, and import the feature table to continue analyses in QIIME 2.

Hope this helps!

2 Likes