Pluging error from composition--anacom

Hi,

I have filtered the table.qza and then using it for ancom analysis, but it shows some error: I will be thankful for your help.

command:
qiime composition ancom --i-table soil-c10-mins2-table.qza --m-metadata-file metadata3.tsv --m-metadata-column Treatment --o-visualization ancom-Soil.treatment.qzv --verbose

error:
Traceback (most recent call last):

File “/opt/gridware/pkg/el6/apps/qiime/2018.11.0/bin/lib/python3.5/site-packages/q2cli/commands.py”, line 274, in call

results = action(**arguments)

File “<decorator-gen-451>”, line 2, in ancom

File “/opt/gridware/pkg/el6/apps/qiime/2018.11.0/bin/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 199, in bound_callable

self.signature.check_types(**user_input)

File “/opt/gridware/pkg/el6/apps/qiime/2018.11.0/bin/lib/python3.5/site-packages/qiime2/core/type/signature.py”, line 301, in check_types

name, kwargs[name].type, spec.qiime_type))

TypeError: Parameter ‘table’ received an argument of type FeatureTable[Frequency]. An argument of subtype FeatureTable[Composition] is required.

Plugin error from composition:

Parameter ‘table’ received an argument of type FeatureTable[Frequency]. An argument of subtype FeatureTable[Composition] is required.

See above for debug info.

Hi @Yogesh_Gupta,
my best guess is that your file ‘soil-c10-mins2-table.qza’ contains ‘0’ counts.
Did you use:
qiime composition add-pseudocount

To preprocess the filtered abundance table?

Best,
Luca

2 Likes

Thanks, after filtering I run qiime composition add-pseudocount and now it is not showing any error.

Thanks
Yogesh

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