qiime feature-table summarize error: list index out of range

Technical Support
1

I am a new QIIME2 user and I have encountered an error while practicing with a collegue’s data. When I try to run the following code:

qiime feature-table summarize
–i-table ivanbc-table-dada2.qza
–o-visualization ivanbc-table-dada2.qzv
–m-sample-metadata-file ivanbc-metadata.tsv
–verbose

I get the following error:

Plugin error from feature-table:

list index out of range

See above for debug info.

Here is the verbose output, sorry for the poor formatting:

/home/qiime2/miniconda/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_feature_table/_summarize/_visualizer.py:122: FutureWarning: The signature of Series.to_csv was aligned to that of DataFrame.to_csv, and argument ‘header’ will change its default value from False to True: please pass an explicit value to suppress this warning.
os.path.join(output_dir, ‘sample-frequency-detail.csv’))
/home/qiime2/miniconda/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_feature_table/_summarize/_visualizer.py:124: FutureWarning: The signature of Series.to_csv was aligned to that of DataFrame.to_csv, and argument ‘header’ will change its default value from False to True: please pass an explicit value to suppress this warning.
os.path.join(output_dir, ‘feature-frequency-detail.csv’))
Traceback (most recent call last):
File “/home/qiime2/miniconda/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/commands.py”, line 311, in call
results = action(**arguments)
File “</home/qiime2/miniconda/envs/qiime2-2019.4/lib/python3.6/site-packages/decorator.py:decorator-gen-330>”, line 2, in summarize
File “/home/qiime2/miniconda/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 231, in bound_callable
output_types, provenance)
File “/home/qiime2/miniconda/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 427, in callable_executor
ret_val = self._callable(output_dir=temp_dir, **view_args)
File “/home/qiime2/miniconda/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_feature_table/_summarize/_visualizer.py”, line 156, in summarize
sample_frequencies
File “/home/qiime2/miniconda/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_feature_table/_summarize/_vega_spec.py”, line 106, in vega_spec
‘value’: metadata_categories[0]
IndexError: list index out of range

This is from phred33V2 formatted data, so it didn’t need an additional demultiplexing step once imported, and gave me output files that worked with dada2 denoising. That FeatureTable is ivanbs-table-dada2.qza. Other output tables from the denoising step have processed successfully, so I’m not sure where the issue is coming from. Thanks in advance!

2

Hi @jameshopkins,

I think the issue is with your metadata, rather than your dada2 data. Could you run the command without the metadata, and report back, please? Maybe check the metadata tutorial to see if you’re having a formatting issue.

Best,
Justine

2 Likes
3

Thanks Justine, that worked! Is my metadata file not necessary for this step?

4

Hi @jameshopkins,

No, metadata isn’t necessary for the feature table summary itself. It just adds to the interpretation and makes life better. But, it will be necessary later, so its probably good to figure out why your metadata isn’t qiime 2 compatible so you can get that sorted sooner.
Best,
Justine