# Augur trait error

**URL:** <https://nextstrain.discourse.group/t/augur-trait-error/867>\
**Category:** Uncategorized\
**Created:** [November 25, 2021, 8:27am UTC](https://nextstrain.discourse.group/t/augur-trait-error/867 "2021-11-25T08:27:21Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![avrajit](https://avatars.discourse-cdn.com/v4/letter/a/9de0a6/32.png) [@avrajit](https://nextstrain.discourse.group/u/avrajit)\
**Post date:** [November 25, 2021, 8:27am UTC](https://nextstrain.discourse.group/t/augur-trait-error/867/1 "2021-11-25T08:27:22Z")

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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

```auto
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

---

<div class="post-metadata">

**Author:** ![rneher](https://yyz1.discourse-cdn.com/flex031/user_avatar/nextstrain.discourse.group/rneher/32/20_2.png) [@rneher](https://nextstrain.discourse.group/u/rneher)\
**Post date:** [December 20, 2021, 8:46pm UTC](https://nextstrain.discourse.group/t/augur-trait-error/867/2 "2021-12-20T20:46:22Z")

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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.

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<div class="post-metadata">

**Author:** ![avrajit](https://avatars.discourse-cdn.com/v4/letter/a/9de0a6/32.png) [@avrajit](https://nextstrain.discourse.group/u/avrajit)\
**Post date:** [December 22, 2021, 6:59am UTC](https://nextstrain.discourse.group/t/augur-trait-error/867/3 "2021-12-22T06:59:50Z")

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