Dear Tech Supporters
I am running qiime2-2019.1 on a virtual linux machine via docker. My virtual machine has 60 GB of RAM and 12 CPU (2 cores per socket > 6 sockets).
I have 195 Samples from 4 MiSeq runs (my imported .qza has 15 GB).
So far everything ran very smoothly (data import and training feature-classifier). Then I started dada2 denoise-paired using the following command:
sudo docker run -t -i -v $(pwd):/data qiime2/core:2019.1 qiime dada2 denoise-paired \
It went through filtering, learning error rates, denoising, and then started chimera removal. After more than 6 days I stopped the command since a colleague who runs qiime2 via docker on a similar linux VM (100GB RAM, 16 CPU) told me for him it takes only ~10h to process 6-7 MiSeq runs (~45GB imported .qza). One of the few clear system differences is that he has 8 cores per socket > 2 sockets. Do you think this is the important difference? I can’t believe the 4 more cores he has makes all the difference from 10h to almost a week (and RAM doesn’t seem to be limiting when looking at the system’s performance).
Thank you so much!