BUG(refine/utils): Uncaught TypeError: '<' not supported between instances of 'NoneType' and 'str' #1086
Description
Current Behavior
Running augur refine I get an uncaught TypeError: '<' not supported between instances of 'NoneType' and 'str'
The error is thrown by write_json from utils.py but the bug should probably be caught in refine already.
Expected behavior
Clear error message that helps me debug
How to reproduce
Here's a simple copy/paste/run reproducible example:
wget https://github.com/nextstrain/augur/files/9914307/nonetype-bug.tar.zst.txt
tar xf nonetype-bug.tar.zst.txt
augur refine --tree results/b1/tree_fixed.nwk --alignment results/b1/masked.fasta --metadata results/b1/metadata.tsv --output-tree results/b1/tree.nwk --root ref_in_coord --divergence-unit mutations --keep-polytomies --use-fft --output-node-data results/b1/branch_lengths.json
Augur 18.1.1 with Python 3.10
cc @victorlin
augur refine is using TreeTime version 0.9.4
190.58 ***WARNING: TreeAnc._check_alignment_tree_gtr_consistency: NO SEQUENCE
FOR LEAF: 'None'
190.58 ***WARNING: TreeAnc._check_alignment_tree_gtr_consistency: NO SEQUENCE
FOR LEAF: 'None'
190.59 ***WARNING: TreeAnc: 2 nodes don't have a matching sequence in the
alignment. POSSIBLE ERROR.
204.88 WARNING: Previous versions of TreeTime (<0.7.0) RECONSTRUCTED sequences
of tips at positions with AMBIGUOUS bases. This resulted in unexpected
behavior is some cases and is no longer done by default. If you want to
replace those ambiguous sites with their most likely state, rerun with
`reconstruct_tip_states=True` or `--reconstruct-tip-states`.
updated tree written to results/b1/tree.nwk
Traceback (most recent call last):
File "/opt/homebrew/Caskroom/miniforge/base/envs/nextstrain/lib/python3.10/site-packages/augur/__init__.py", line 66, in run
return args.__command__.run(args)
File "/opt/homebrew/Caskroom/miniforge/base/envs/nextstrain/lib/python3.10/site-packages/augur/refine.py", line 316, in run
write_json(node_data, node_data_fname)
File "/opt/homebrew/Caskroom/miniforge/base/envs/nextstrain/lib/python3.10/site-packages/augur/utils.py", line 127, in write_json
json.dump(data, handle, indent=indent, sort_keys=sort_keys)
File "/opt/homebrew/Caskroom/miniforge/base/envs/nextstrain/lib/python3.10/json/__init__.py", line 179, in dump
for chunk in iterable:
File "/opt/homebrew/Caskroom/miniforge/base/envs/nextstrain/lib/python3.10/json/encoder.py", line 431, in _iterencode
yield from _iterencode_dict(o, _current_indent_level)
File "/opt/homebrew/Caskroom/miniforge/base/envs/nextstrain/lib/python3.10/json/encoder.py", line 405, in _iterencode_dict
yield from chunks
File "/opt/homebrew/Caskroom/miniforge/base/envs/nextstrain/lib/python3.10/json/encoder.py", line 353, in _iterencode_dict
items = sorted(dct.items())
TypeError: '<' not supported between instances of 'NoneType' and 'str'
An error occurred (see above) that has not been properly handled by Augur.
To report this, please open a new issue including the original command and the error above:
<https://github.com/nextstrain/augur/issues/new/choose>