AttributeError: 'NoneType' object has no attribute 'remove'

[sinamajidian]

orthoxml-tools filter --infile FastOMA_HOGs_Feb2026_raw.orthoxml  --strategy cascade-remove  --threshold 0.3 --outfile out0.3.orthoxml 

Traceback (most recent call last):
  File "fastoma/bin/orthoxml-tools", line 7, in <module>
    sys.exit(main())
  File "fastoma/lib/python3.9/site-packages/orthoxml/cli.py", line 369, in main
    args.func(args)
  File "fastoma/lib/python3.9/site-packages/orthoxml/cli.py", line 201, in handle_filter
    filter_hogs(args.infile, args.outfile, args.threshold,
  File "fastoma/lib/python3.9/site-packages/orthoxml/streamfilters.py", line 216, in filter_hogs
    process_stream_orthoxml(source_orthoxml,
  File "fastoma/lib/python3.9/site-packages/orthoxml/parsers.py", line 196, in process_stream_orthoxml
    for tag, elem in parser.parse():
  File "fastoma/lib/python3.9/site-packages/orthoxml/parsers.py", line 138, in parse
    if (result := self.process_toplevel_group(elem)) is not None:
  File "fastoma/lib/python3.9/site-packages/orthoxml/streamfilters.py", line 107, in process_toplevel_group
    parent.remove(h)
AttributeError: 'NoneType' object has no attribute 'remove'

The raw orthoxml is in my Curnagl work folder at default/smajidi1/bird_project/fastoma_6feb2026/Output/filtering/FastOMA_HOGs_Feb2026_raw.orthoxml

Perhaps @ali-yz or @nromashchenko could take a look at this error. Thank you in advance

[sinamajidian]

With --strategy extract, the output file is bigger than the input file (3GB vs 2.3GB). For example the gene id 1053013941 appears two times in the output orthoXML

 $ grep 1053013941  FastOMA_HOGs_Feb2026_orthoXMLtools_extract_0.3.orthoxml 
        <gene id="1053013941" protId="CALSQU_R06387"/>
        <geneRef id="1053013941"/>
                                    <geneRef id="1053013941"/>

I ran this:

orthoxml-tools filter --infile FastOMA_HOGs_Feb2026_raw.orthoxml  --strategy extract  --threshold 0.3 --outfile FastOMA_HOGs_Feb2026_orthoXMLtools_extract_0.3.orthoxml