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bowmanjeffs / paprica

paprica - PAthway PRediction by phylogenetIC plAcement
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SettingWithCopyWarning: harmless or a bigger problem? #67

Closed Gustius closed 5 years ago

Gustius commented 5 years ago

At the end of running paprica-run.sh, I get some warnings. Are these just harmless or do I have a problem? Here the last lines of the output where these warnings appear:

Normalizing abundance for unique sequences... /home/gust/.local/lib/python2.7/site-packages/pandas/core/indexing.py:362: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy self.obj[key] = _infer_fill_value(value) /home/gust/.local/lib/python2.7/site-packages/pandas/core/indexing.py:543: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy self.obj[item] = s /home/gust/.local/lib/python2.7/site-packages/pandas/core/frame.py:3697: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame

See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy errors=errors) Thanks for using paprica! Please be sure to read through the manual, and check out the tutorials at www.polarmicrobes.org

bowmanjeffs commented 5 years ago

These are just warnings, there are no issues. They seem to be generated internally by different functions within Python, as I've fixed all warnings that cite a location in the paprica scripts.