I tried to run beta diversity analysis through the standard qiime 2 workflow and I got the following error
tests-MacBook-Pro-4:data mortonjt$ qiime diversity beta --i-table palmspaper_targeted_filtered_sampleids_matched.qza --p-metric braycurtis --o-distance-matrix palm_ms_bray --verbose Traceback (most recent call last): File "/Users/mortonjt/miniconda3/envs/bio/lib/python3.5/site-packages/q2cli-2017.2.0-py3.5.egg/q2cli/commands.py", line 217, in __call__ results = action(**arguments) File "<decorator-gen-145>", line 2, in beta File "/Users/mortonjt/miniconda3/envs/bio/lib/python3.5/site-packages/qiime2-2017.2.0-py3.5.egg/qiime2/sdk/action.py", line 151, in callable_wrapper self.signature.check_types(**user_input) File "/Users/mortonjt/miniconda3/envs/bio/lib/python3.5/site-packages/qiime2-2017.2.0-py3.5.egg/qiime2/core/type/signature.py", line 282, in check_types " %r." % (name, spec.qiime_type)) TypeError: Argument to input 'table' is not a subtype of FeatureTable[Frequency] % Properties(['uniform-sampling']).
A couple of questions
- Am I getting this error because
qiime diversity betaexpects rarified a
- If the above is true, Is it possible to relax / extend this to other normalization schemes such as total sum scaling? There are cases where rarefaction is computationally intractable and impracticable. For instance, running rarefaction on metabolomics data will completely kill the RAM, since these are very high abundances.