`qiime demux summarize` with aligned representative sequences

[Bing (Jinbing Bai)]

Hi,
I have filtered part of data from AGP dataset. All the sequences are aligned and demultiplexed. I tried to summarize the results and got the following errors:

    `(qiime2-2017.6) Jinbings-iMac:agp jinbingbai$ ls
BingQiime.pem.txt			Raw data				sample_id_list_filtered_seqs.fna
File archives				agp-metadata.tsv
Qiime2Bing AWS notes 6-13-2017.docx	aligned-agp-sequences.qza

  (qiime2-2017.6) Jinbings-iMac:agp jinbingbai$ qiime demux summarize --i-data aligned-agp-sequences.qza --o-visualization agp-sequence.qzv --verbose
    Traceback (most recent call last):
      File "/Users/jinbingbai/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/q2cli/commands.py", line 222, in __call__
        results = action(**arguments)
      File "<decorator-gen-147>", line 2, in summarize
      File "/Users/jinbingbai/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/qiime2/sdk/action.py", line 176, in callable_wrapper
        self.signature.check_types(**user_input)
      File "/Users/jinbingbai/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/qiime2/core/type/signature.py", line 283, in check_types
        " %r." % (name, spec.qiime_type))
    TypeError: Argument to input 'data' is not a subtype of SampleData[PairedEndSequencesWithQuality | SequencesWithQuality].

    Plugin error from demux:

      Argument to input 'data' is not a subtype of
      SampleData[PairedEndSequencesWithQuality | SequencesWithQuality].

    See above for debug info.
    (qiime2-2017.6) Jinbings-iMac:agp jinbingbai$ source deactivate qiime2.2017.6`

Thanks,
Bing

[jairideout (Jai Ram Rideout)]

Hi @Bing! demux summarize accepts demultiplexed sequences of type SampleData[SequencesWithQuality] or SampleData[PairedEndSequencesWithQuality]. This type of data is produced by demux emp-single or demux emp-paired, or by importing your data in a supported format.

aligned-agp-sequences.qza likely has the type FeatureData[AlignedSequence], which isn’t supported by qiime demux summarize. The visualization is designed for inspecting the quality scores of your raw sequence data, and your aligned representative sequences don’t have quality scores associated with them at this stage.

As of the latest QIIME 2 release (2017.6) you can use qiime metadata tabulate to inspect your aligned representative sequences. For example:

qiime metadata tabulate --m-input-file aligned-agp-sequences.qza --o-visualization tabulated-seqs.qzv

The resulting .qzv file can be viewed with qiime tools view or at view.qiime2.org.