Is it possible to query the Open Tree directly?
gaurav opened this issue · comments
I was able to run a PhyloNext analysis on GBIF using the Acacia_Mishler,2014_Latin-labels.nwk tree on Australia without any problems: https://phylonext.gbif.org/run/eeb8f380-5716-4e47-bb72-2ba6de29da91
I have been trying to use PhyloNext to use the synthetic Open Tree to look up patterns of distribution in the genus Erica in Africa. However, this consistently fails for me (see e.g. https://phylonext.gbif.org/run/d8c5b4ea-abb7-455d-9184-1d53403b2e95). Is this because 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. Is that incorrect? If leaving these two fields empty is what caused the Internal Server Error in the results, then the form should make that clearer (by making one of those fields required, or by adding a note to indicate that one of those fields need to be filled in); otherwise, let me know and I'll send you the pipeline arguments I provided for that run so we can figure out why it's resulting in an Internal Server Error.
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.
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.
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.
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.
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.