(1/1?) no such option: --p-parttree

I’m a beginner to qiime 2.
In a study of phylogeny using this command, I got a error message below.

$ qiime phylogeny align-to-tree-mafft-fasttree \

–i-sequences rep-seqs.qza
–o-alignment aligned-rep-seqs.qza
–o-masked-alignment masked-aligned-rep-seqs.qza
–o-tree unrooted-tree.qza
–o-rooted-tree rooted-tree.qza
Plugin error from phylogeny:

The number of sequences in your feature table is larger than 1 million, please use the parttree parameter

Then, I tried following command, but got another error.

$ qiime phylogeny align-to-tree-mafft-fasttree \

–i-sequences rep-seqs.qza
–p-parttree
–o-alignment aligned-rep-seqs.qza
–o-masked-alignment masked-aligned-rep-seqs.qza
–o-tree unrooted-tree.qza
–o-rooted-tree rooted-tree.qza

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!

1 Like

Hey @iwmtpione!

Welcome to the forum!

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:

  1. 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.

  2. Use q2-fragment-insertion instead which will perform SEPP to create a nicer phylogenetic tree. Documentation is here for that.

Hope that helps!

Thank you ebolyen.
According to your assistance, I succeeded to start mafft program by following command.

$ qiime alignment mafft \

–i-sequences rep-seqs.qza
–o-alignment aligned-rep-seqs.qza
–p-parttree
Plugin error from alignment:

Command ‘[‘mafft’, ‘–preservecase’, ‘–inputorder’, ‘–thread’, ‘1’, ‘–parttree’, ‘/tmp/qiime2-archive-6ia55znx/77c3aca1-c9ef-4870-8c7b-21fc8bb72ca0/data/dna-sequences.fasta’]’ returned non-zero exit status 1.

Debug info has been saved to /tmp/qiime2-q2cli-err-d8dv09oz.log

But, 54 hours later, the mafft program stopped with another error message shown above.
It appears due to unknown bug.
Is there any solution?

Hey @iwmtpione,

Could you share this log file /tmp/qiime2-q2cli-err-d8dv09oz.log (assuming the machine hasn’t rebooted in the interim).

Thanks!