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biocore / empress

A fast and scalable phylogenetic tree viewer for microbiome data analysis
BSD 3-Clause "New" or "Revised" License
45 stars 31 forks source link

Standalone raises incorrect parameter error #520

Closed ericap258 closed 3 years ago

ericap258 commented 3 years ago

@gibsramen

Hi empress team,

When using the standalone version, a wrong error message occurs. i.e. I tried to run the following, but got an error message indicating that I was missing the --p-filter-missing-features flag. !empress community-plot \ --tree tree.nwk \ --table 61337_reference-hit.biom \ --sample-metadata 1070_20170412-111709.txt \ --output-dir community-tree-viz3

Error message: File "/opt/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/empress/tools.py", line 247, in match_inputs "The feature table contains features that aren't present as " empress.tools.DataMatchingError: The feature table contains features that aren't present as tips in the tree. You can override this error by using the --p-filter-missing-features flag.

The message should reflect the difference between standalone and qiime 2.

I'd like to try fix this issue if that's possible. Thank you.

kwcantrell commented 3 years ago

Thanks @ericap258! Let me know if you have any questions!