q2-health-index: cannot do slice indexing on <class 'pandas.core.indexes.base.Index'> with these indexers [0.0] of <class 'numpy.float64'>

Hello qiime users!

I’m testing the q2-health-index plugin, but I didn’t find an example or a tutorial. I tried to run this command:

qiime health-index calculate-gmhi --i-table table.qza --m-metadata-file metadata-file.tsv --p-healthy-states saudavel --p-non-healthy-states rest --p-healthy-column condition --o-gmhi-results gmhi_output --o-gmhi-plot gmhi_plot --verbose

I noticed some errors. The last one was this:

“Plugin error from health-index:
cannot do slice indexing on <class ‘pandas.core.indexes.base.Index’> with these indexers [0.0] of <class ‘numpy.float64’>
See above for debug info.”

Has anyone used this metric/plugin and faced this error?

Hi @rraf ! Welcome to the forum.

Thanks for posting – I have never heard of this plugin before and it is not listed in the QIIME 2 library, where community developed plugins are listed, so thanks for putting this on our radar.

The github repository for this plugin does not list very specific info, including where to get support, but I recommend posting an issue on their to get support — the authors are welcome to support your question here, but I am just guessing that they are more likely to monitor their Github than this forum. :man_shrugging:

Good luck!


Hi @Nicholas_Bokulich , thank you very much for the reply!
I will try to get in touch with the developer through github. I would like to ask if you know another q2-plugin or alternative to calculate the GMHI index (https://www.nature.com/articles/s41467-020-18476-8)??

I do not — this index looks very specific to that paper (where it is newly defined). The code is shared in that paper so that is the first place that I would look.

Good luck!

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