Why can't I retrieve the subtree for Lycopodiidae

[rossmounce]

I thought I'd split-up my query (to get Tracheophytes) into smaller groups but I'm still running into problems: Why can't I retrieve the subtree for Lycopodiidae ?

> mono_id <- tnrs_match_names("Lycopodiidae")
> mono_id
  search_string  unique_name approximate_match  ott_id is_synonym flags
1  lycopodiidae Lycopodiidae             FALSE 6133720      FALSE      
  number_matches
1              1
> mono_tree <- tol_subtree(ott_id = ott_id(mono_id))
Error: HTTP failure: 400
Could not find any synthetic tree nodes corresponding to the OTT id provided (6133720).BadInputExceptionorg.neo4j.server.rest.repr.BadInputExceptionlist("opentree.plugins.tree_of_life_v3.doSubtree(tree_of_life_v3.java:658)", "opentree.plugins.tree_of_life_v3.subtree(tree_of_life_v3.java:563)", "java.lang.reflect.Method.invoke(Method.java:498)", "org.neo4j.server.plugins.PluginMethod.invoke(PluginMethod.java:57)", "org.neo4j.server.plugins.PluginManager.invoke(PluginManager.java:168)", "org.neo4j.server.rest.web.ExtensionService.invokeGraphDatabaseExtension(ExtensionService.java:300)", "org.neo4j.server.rest.web.ExtensionService.invokeGraphDatabaseExtension(ExtensionService.java:122)", 
    "java.lang.reflect.Method.invoke(Method.java:498)", "org.neo4j.server.rest.security.SecurityFilter.doFilter(SecurityFilter.java:112)")

[fmichonneau]

This is related to "Why are OTT IDs discovered with rotl missing from an induced subtree?" in the vignette: https://cran.r-project.org/web/packages/rotl/vignettes/how-to-use-rotl.html

I can't investigate right at this minute an alternative, but you'd need to find a node below or above that is monophyletic in the open tree.

[josephwb]

@rossmounce I may be missing something, but the reason is that Lycopodiidae is not found to be monophyletic in the synthetic tree. See here.

[josephwb]

Ack. @fmichonneau beat me by 2 seconds!

[rossmounce]

I found it here (by GUI browsing down the tree on the website) but i note the OTT id appears to be different:
https://tree.opentreeoflife.org/opentree/opentree8.0@ott5602224/Lycopodiidae

6133720 != 5602224

[josephwb]

Welp. I have no idea what that could be... Will ping OT folks.

[josephwb]

When I query the taxonomy things get even weirder.

[rossmounce]

the other ID is queryable by that method: https://tree.opentreeoflife.org/taxonomy/browse?id=6133720

[josephwb]

@rossmounce Ok it seems that the tree and taxonomy are unfortunately currently out of sync. Trying to find ETA on fix.

[josephwb]

Pinging @kcranston on ETA.

[rossmounce]

Well, I'm going to sleep now, so you've got at least 12 hours. Or you can just lob me the 'Tracheophyta' clade which is what I really want 😃

[josephwb]

Regardless, this is clearly an upstream OT problem, not a rotl problem.