I ran ‘qiime phylogeny align-to-tree-mafft-fasttree --i-sequences feature-rep-seq.qza --o-alignment aligned-rep-seqs.qza --o-masked-alignment masked-alignment-rep-seqs.qza --o-tree unrooted-tree.qza --verbose --o-rooted-tree rooted-tree.qza’ and got the following Plugin Error:
Plugin error from phylogeny:
The number of sequences in your feature table is larger than 1 million, please use the parttree parameter
I have tried the same command with the flag --parttree and --p-parttree which resulted in a ‘no such option’-error. Since I could not find any other way of using the parttree parameter in the Forum, I now wonder if I overlooked something??
(P.S. I am using qiime2 version 2019.4.0)