Error when generating PCoA plot

emperor

(Jia Zhou) #1

Hi,

I filtered my distance matrix based on Metadata. Then I wanted to generate PCoA with the filtered distance matrix, but I got an error. Could you please help me to figure it out? Here are the codes I used and the error message.

qiime diversity filter-distance-matrix
–i-distance-matrix core-metrics-results/unweighted_unifrac_distance_matrix.qza
–m-metadata-file MetaData_CaneToadData1.tsv
–p-where “SampleTypes=‘large_intestine’”
–o-filtered-distance-matrix core-metrics-results/large_intestine-filtered-distance-matrix.qza

qiime emperor plot
–i-pcoa core-metrics-results/large_intestine-filtered-distance-matrix.qza
–m-metadata-file MetaData_CaneToadData1.tsv
–p-custom-axes Location
–o-visualization core-metrics-results/PCOA_large_intestine-filtered_unweighted-unifrac-Location.qzv

(qiime2-2018.11) JiadeMacBook-Pro:QIIME2 jiazhou$ less /var/folders/v9/gy5c6y6j3b9cz3f2ccj5lj0m0000gn/T/qiime2-q2cli-err-f97vxur1.log

Traceback (most recent call last):
_ File “/Users/jiazhou/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/q2cli/commands.py”, line 274, in call_
**_ results = action(arguments)_
_ File “”, line 2, in plot_
_ File “/Users/jiazhou/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 199, in bound_callable_
**_ self.signature.check_types(user_input)_
_ File “/Users/jiazhou/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/core/type/signature.py”, line 301, in check_types_
_ name, kwargs[name].type, spec.qiime_type))_
TypeError: Parameter ‘pcoa’ received an argument of type DistanceMatrix. An argument of subtype PCoAResults is required.

Thanks,

Jia


(Jia Zhou) #2

Hi,

I realised I forgot to run one step qiime diversity pcoa before generating qiime emperor plot

Thanks,

Jia


(system) closed #3

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