"No nesting structure in HOGs defined in OrthoXML"

[nromashchenko]

Version: 2.1.0

I am trying to make a database from orthoxml from the fastoma's example data:

omamer mkdb --db testdata.h5 --log_level debug --orthoxml expected_output/FastOMA_HOGs.orthoxml --sequences in_folder/proteome/*.fa 
 --species_tree in_folder/species_tree.nwk 

this breaks with

...

WARNING: No nesting structure in HOGs defined in OrthoXML.

...

    raise tables.NoSuchNodeError(
tables.exceptions.NoSuchNodeError: Path not found in database (/ChildrenHOG)
...

And in the code, the warning in question has a todo note to check things more carefully if there is no nesting structure. However there are subHOGs in the example file, for example:

<orthologGroup id="HOG:0000004_1" taxonId="1">
  <score id="CompletenessScore" value="1.0" />
  <property name="OMAmerRootHOG" value="HOG:E0990677" />
  <property name="TaxRange" value="inter2" />
  <geneRef id="1000000002" />
  <orthologGroup id="HOG:0000004_2" taxonId="2">
    <score id="CompletenessScore" value="1.0" />
    <property name="TaxRange" value="inter1" />
    <geneRef id="1002000004" />
    <geneRef id="1001000004" />
  </orthologGroup>
</orthologGroup>

I also see the same error if I try toy files from the orthoxml standard (I tried ex1 and ex2. They require changing "geneId" to "protId" which is a separate issue btw).