There was a problem with the command:
(1/1?) no such option: --p-parttree
I would like to learn correct command line.
The feature table is outputted from a seqs.fna file composed of almost 25 million reads, but I want to analyze at once, if available.
Please suggest me good resolution about this problem.
Thanks!
So this error comes from mafft which is part of the align-to-mafft-fasttree pipeline. The parameter you constructed is totally correct, but that pipeline doesn’t know how to pass it onwards to mafft.
You have two pretty good options here:
Run each step of the pipeline manually instead. You can find the code that represents the pipeline here. I think it’s pretty readable, but I happen to know Python pretty well. Roughly, you would run qiime alignment mafft (this is where --p-parttree goes), then qiime alignment mask, then qiime phylogeny fasttree, and then qiime phylogeny midpoint-root.
Use q2-fragment-insertion instead which will perform SEPP to create a nicer phylogenetic tree. Documentation is here for that.