Is it possible to query the Open Tree directly? about phylonext HOT 5 OPEN

Hello @gaurav

Thank you for reporting this issue.

Unfortunately, the error message (Internal Server Error) is not very informative, and the downloadable results appear to be empty. According to the log file, it seems that even the first process of the pipeline hasn't started.

I attempted to configure the analysis for Erica species in Africa myself but encountered the same error. Therefore, it's likely that the issue is related to the PhyloNext server (https://github.com/gbif/phylonext-ws). I will report this to the main server developer.

In the meantime, if you wish, you can run the analysis via the command line. However, you will need to download a local copy of the data from GBIF (e.g., the Erica subset). Please let me know if you require any guidance.

Thanks again for bringing this issue to our attention.
We will investigate and resolve it as soon as possible.

from phylonext.

I neither chose a OToL tree in the "Choose a predefined tree from OTL" field on the form nor entered a phylogeny in the "Phylogenetic tree in newick format (phytree param)" field? I assumed that if I left both of these fields empty, then PhyloNext would look up the occurrence data as per the phylogenetic filters and then pick up the minimum tree for those taxa from OpenTree.

If you do not specify a phylogenetic tree, PhyloNext will automatically fetch one from the OpenTree.
However, you need to specify the type of phylogenetic tree labels as Latin.

We will add a note to the GUI to clarify this point and apologize for any confusion caused.
In future versions, we may introduce an auto-detection feature to simplify this process.

from phylonext.

PS. It appears that there are no age estimates for Erica in OpenTree. Therefore, you will need to set the --maxage parameter to some value. However, this parameter is currently not available in the GUI.

from phylonext.

I attempted to retrieve a tree for Erica from OpenTree, but unfortunately, there's insufficient data to estimate dates. This means that the task cannot be completed automatically, and you'll need to construct the tree manually.

from phylonext.

Hello @gaurav,

We found that the problem is related with OpenTree, where the genus Erica was completely missing from the taxonomic backbone.

Thankfully, the genus has now been added back into the synthetic tree, but now it only includes only 3 tree tips:
https://tree.opentreeoflife.org/opentree/argus/ottol@3546862/Erica

Unfortunately, this means we can't automatically retrieve the full Erica tree from OToL.
However, I hope that the OToL team will include all Erica species in their next update.

from phylonext.