Error when running with greengenes taxonomy files, integer ID field causes type issue

[mstapylton]

ID column only containing integers causes the dataframe index to be int type which causes the index.intersection code to fail in tool.py: reproduce-files.zip Here's the fix I put in where I cast the index to type string:

[ElDeveloper]

Thanks @mstapylton, would you be able to submit a pull request with these changes and a new unit test?

[mstapylton]

Sure, I think I can carve out some time next week to put together a PR. I work in the Clemente lab by the way.

[ElDeveloper]

That is absolutely wonderful to hear. Thanks so much, let us know if you need any help, and say hi to Jose! 👋

On Jul 16, 2021, at 7:19 AM, mstapylton @.***> wrote:

Sure, I think I can carve out some time next week to put together a PR. I work in the Clemente lab by the way.

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[fedarko]

Thank you for the detailed information and bug report, @mstapylton!

I downloaded the files you uploaded and tried running Empress using them; I don't know if this will help with the PR / testing, but the behavior I get (using the latest version of Empress as of today, and on my system) seems a bit different from the error message you screenshot here. I'm recording these differences below, just in case it's helpful to you or to future users.

• When running Empress standalone (as is done in the issue here), I instead get the following error:

  Traceback (most recent call last):
    File "/home/marcus/Software/miniconda2/envs/qiime2-2021.2/bin/empress", line 11, in <module>
      load_entry_point('empress', 'console_scripts', 'empress')()
    File "/home/marcus/Software/miniconda2/envs/qiime2-2021.2/lib/python3.6/site-packages/click/core.py", line 829, in __call__
      return self.main(*args, **kwargs)
    File "/home/marcus/Software/miniconda2/envs/qiime2-2021.2/lib/python3.6/site-packages/click/core.py", line 782, in main
      rv = self.invoke(ctx)
    File "/home/marcus/Software/miniconda2/envs/qiime2-2021.2/lib/python3.6/site-packages/click/core.py", line 1259, in invoke
      return _process_result(sub_ctx.command.invoke(sub_ctx))
    File "/home/marcus/Software/miniconda2/envs/qiime2-2021.2/lib/python3.6/site-packages/click/core.py", line 1066, in invoke
      return ctx.invoke(self.callback, **ctx.params)
    File "/home/marcus/Software/miniconda2/envs/qiime2-2021.2/lib/python3.6/site-packages/click/core.py", line 610, in invoke
      return callback(*args, **kwargs)
    File "/home/marcus/Dropbox/Work/KnightLab/Empress/fedarko/empress/empress/scripts/_cli.py", line 46, in tree_plot
      shear_to_feature_metadata=shear_to_feature_metadata)
    File "/home/marcus/Dropbox/Work/KnightLab/Empress/fedarko/empress/empress/core.py", line 158, in __init__
      shear_to_feature_metadata,
    File "/home/marcus/Dropbox/Work/KnightLab/Empress/fedarko/empress/empress/core.py", line 244, in _validate_and_match_data
      ) = match_tree_and_feature_metadata(self.tree, self.features)
    File "/home/marcus/Dropbox/Work/KnightLab/Empress/fedarko/empress/empress/tools.py", line 87, in match_tree_and_feature_metadata
      "No features in the feature metadata are present in the tree, "
  empress.tools.DataMatchingError: No features in the feature metadata are present in the tree, either as tips or as internal nodes.

  This is still a bug in Empress (the feature metadata does match up with the tree, so this error is incorrect!), but it's a different error to the one you show above (ValueError: invalid literal for int() with base 10: '35bf...').

  I assume the dataset used in the screenshot is different from the dataset included in the ZIP file, which might explain the difference in error messages. However I'm still confused by the traceback you showed, since the btt = [int(s) for s in btt] line listed there doesn't appear anywhere in Empress' codebase (at least as far as I can tell?), even in old releases.

• When I run Empress through QIIME 2*, I don't run into this problem -- I'm able to create and load a visualization without any problems.

  * (after first importing the tree file into a QZA with the following command: qiime tools import --type "Phylogeny[Rooted]" --input-path 99_otus.tree --output-path 99_otus.qza)

Anyway -- it's not a huge deal or anything, but hopefully this provides some extra context if these problems were coming up during creation of the PR / testing. Thank you again for raising this issue.