I’ve been trying to work out a smooth method to analyze a large data set of sequences. In short, it contains 30 samples with 389,340 features and a total frequency of 2,877,374.
I expect this data set to take a while to run through the QIIME 2 workflow, especially in processes necessary to generate the tree but another person was able to run the data through QIIME 1 within a day. Looking at the mask step alone, I’ve had it running 4 days through command line.
qiime alignment mafft
qiime alignment mask
qiime phylogeny fasttree
I’ve also attempted to use qiime fragment-insertion sepp
using default parameters to no avail.
Can anyone suggest what I might be doing incorrect in comparison to their QIIME 1 run?
Thank you for any suggestions or comments.