Hope you are fine
thanks for quick response
I ran the command and seems it would work, but now the error it is giving is related to tree
There was a problem with the command:
(1/1) Invalid value for “–i-phylogeny”: Expected an artifact of at least
type Phylogeny[Rooted]. An artifact of type Phylogeny[Unrooted] was
Can you please let me know how to create rooted tree.
thanks in advance
Can I get the full command you ran and the version of QIIME2 you are using. Also if I could get the command you ran to get your unroot tree that would be helpful as well.
I am not really able to answer your question with out more information.
Hlo Again chloe
Well I am using qiime2.2019
because of the reason picrust2 plugin was installed.
Regarding the command i used was
qiime diversity core-metrics-phylogenetic --i-phylogeny phylogeny/S1_fast.tree.qza --m-metadata-file metadataS1.tsv --i-table S1_final/clustered_table_cr-97.qza --p-sampling-depth 1 --output-dir S1_core_1
and it gave the error. Unrooted tree was used.
There are a lot of ways to generate phylogenies for qiime2 for more information we have a great in depth phylogeny tutorial that you might find really helpful.
I am not sure how you generated your phylogeny but I think our phylogeny midpoint command might be what you are looking for.
This command takes an unrooted tree(like the one you have) and outputs a rooted phylogeny by rooting your phylogeny roughly in the middle of your data.
Hope that helps!
thanks for your positive and quick responses
Well I followed the same tutorial and developed the tree by fast-tree method but now the main command is error (as posted earlier).
I am really in a bit of bother regarding this. If you can help me out I will send you my files personally.
I am sorry you are getting frustrated at this error. I currently don’t have enough information to help you.
- I am not sure what the main command error is that you posted earlier. Are you saying that you got
(1/1) Invalid value for“–i-phylogeny”: Expected an artifact of at leasttype Phylogeny[Rooted]. An artifact of type Phylogeny[Unrooted] was providedagain?
- I don’t know if you ran the midpoint command like I suggest above? If you have an unrooted tree that is the easiest way to get a rooted tree
- Any commands that you have run to generate the tree/ remediate the fact that it is unrooted would be helpful.
If you used fast-tree to generate your phylogeny then you have an unrooted tree and I would again recommend running the mid-point command to get a rooted tree.
Feel free to post any files you have that tends to give me more information. However I am not able to fix your files for you only suggest solutions for you to implement.
Hope this helps
A post was split to a new topic: Plugin error from diversity: None of the sample identifiers match between the metadata and the coordinates.