qiime2 / q2-diversity

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`beta` not capable of handling `wminkowski`, `mahalanobis` #288

Closed ChrisKeefe closed 4 years ago

ChrisKeefe commented 4 years ago

Bug Description Beta diversity calculations using these two metrics fail. wminkowski takes an extra parameter, and has been deprecated in favor of the "weighted version of minkowski". mahalanobis produces a numpy.linalg.LinAlgError: Singular Matrix error, when handed any of a number of frequently-used test-data sets (crawford, moving pictures, and a minimal example).

Steps to reproduce the behavior

  1. Load a qiime2 env, and run:
    qiime diversity beta \
    --i-table table.qza \
    --p-metric <insert-metric-here> \
    --o-alpha-diversity <metric-name>.qza

    passing a valid feature table. See the resulting error message.

Computation Environment

Approach