Augur trait error

1

Hi I was using nextstrain tutorial for covid data analysis with a dataset I downloded form GSAID.

I completed till refining stage with augur refine but got stuck in augur trait. I am using
Ubuntu 20, 64 bit
augur version 13.0.3 with anaconda3 installation and updates
the command I used is below

augur traits --tree result/tree.nwk --metadata 1637054504304.metadata.tsv --output-node-data result/trait.json --columns region country --confidence

The error is below

raceback (most recent call last):
  File "/home/anaconda3/envs/nextstrain/bin/augur", line 10, in <module>
    sys.exit(main())
  File "/home/anaconda3/envs/nextstrain/lib/python3.8/site-packages/augur/__main__.py", line 10, in main
    return augur.run( argv[1:] )
  File "/home/anaconda3/envs/nextstrain/lib/python3.8/site-packages/augur/__init__.py", line 75, in run
    return args.__command__.run(args)
  File "/home/anaconda3/envs/nextstrain/lib/python3.8/site-packages/augur/traits.py", line 132, in run
    traits, columns = read_metadata(args.metadata)
  File "/home/anaconda3/envs/nextstrain/lib/python3.8/site-packages/augur/utils.py", line 81, in read_metadata
    return MetadataFile(fname, query, as_data_frame).read()
  File "/home/anaconda3/envs/nextstrain/lib/python3.8/site-packages/augur/util_support/metadata_file.py", line 22, in read
    self.check_metadata_duplicates()
  File "/home/anaconda3/envs/nextstrain/lib/python3.8/site-packages/augur/util_support/metadata_file.py", line 60, in check_metadata_duplicates
    self.metadata[self.key_type]
  File "/home/anaconda3/envs/nextstrain/lib/python3.8/site-packages/pandas/core/frame.py", line 4060, in query
    res = self.eval(expr, **kwargs)
  File "/home/anaconda3/envs/nextstrain/lib/python3.8/site-packages/pandas/core/frame.py", line 4191, in eval
    return _eval(expr, inplace=inplace, **kwargs)
  File "/home/anaconda3/envs/nextstrain/lib/python3.8/site-packages/pandas/core/computation/eval.py", line 353, in eval
    ret = eng_inst.evaluate()
  File "/home/anaconda3/envs/nextstrain/lib/python3.8/site-packages/pandas/core/computation/engines.py", line 80, in evaluate
    res = self._evaluate()
  File "/home/anaconda3/envs/nextstrain/lib/python3.8/site-packages/pandas/core/computation/engines.py", line 121, in _evaluate
    return ne.evaluate(s, local_dict=scope)
  File "/home/anaconda3/envs/nextstrain/lib/python3.8/site-packages/numexpr/necompiler.py", line 823, in evaluate
    signature = [(name, getType(arg)) for (name, arg) in
  File "/home/anaconda3/envs/nextstrain/lib/python3.8/site-packages/numexpr/necompiler.py", line 823, in <listcomp>
    signature = [(name, getType(arg)) for (name, arg) in
  File "/home/anaconda3/envs/nextstrain/lib/python3.8/site-packages/numexpr/necompiler.py", line 705, in getType
    raise ValueError("unknown type %s" % a.dtype.name)
ValueError: unknown type object

Please help.
Thanks

2

this error is somewhere while parsing the metadata file with pandas. I believe we have seen this before and it was related to a specific pandas version. I’ll post here if I find the prior issue.

3

Thanks. I also doubt that and it worked in my lab system which have different conda environment.