Problem with getting Metadata from a QIIME 2 artifact

[savan]

Hello, I am trying to get metadata from my artifact file (.qza), the command as:

qiime metadata tabulate
--m-input-file bioreactor.qza
--o-visualization bioreactor-metadata.qzv

however, it came out:
There was an issue with viewing the artifact bioreactor.qza as QIIME 2 Metadata:

Artifact <artifact: SampleData[PairedEndSequencesWithQuality] uuid: f2f577c8-786e-4f6a-980b-0a4d0269f427> cannot be viewed as QIIME 2 Metadata.

[thermokarst]

Hi @savan - that warning is telling you that QIIME 2 isn't aware of a way to interpret (or view) that type of data as metadata.

If you are trying to visualize SampleData[PairedEndSequencesWithQuality], I would recommend checking out the demux summarize visualization, that should get you moving!

Keep us posted!

[savan]

Hi @thermokarst, the artifact file barcode.qza was imported as format-Casava 1.8 paired-end demultiplexed fastq:

qiime tools import
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path gzsample
--source-format CasavaOneEightSingleLanePerSampleDirFmt
--output-path bioreactor.qza

My understand is I don't need to demultiplex the sequence reads, right? So the next step should be see summary and look at the sequence quality. However, no matter I use

qiime demux summarize
--i-data bioreactor.qza
--o-visualization bioreactor.qzv

or
qiime dada2 denoise-paired
--i-demultiplexed-seqs bioreactor.qza
--o-table table
--o-representative-sequences rep-seqs
--p-trim-left-f 13
--p-trim-left-r 13
--p-trunc-len-f 150
--p-trunc-len-r 150

it all shows - Error: Got unexpected extra arguments.

Could you please help me to figure out how to get moving forward?

Thank you very much!

[thermokarst]

Hi @savan!

@savan

it all shows - Error: Got unexpected extra arguments.

That looks like a shell error - it certainly isn't a QIIME 2 error! Did you copy and paste your command here exactly as you ran? If so, it looks like you might be missing the backslashes at the end of your lines:

qiime demux summarize \
  --i-data bioreactor.qza \
  --o-visualization bioreactor.qzv

These tell your shell to escape the newline characters, allowing you to write a command across many lines.

Alternatively, you could put it all on one line:

qiime demux summarize --i-data bioreactor.qza --o-visualization bioreactor.qzv

The choice is entirely up to you! We like to spread across multiple lines in our tutorials and documentation because we think it makes things easier to read, but doesn't serve any functional purpose. Hope that helps - keep us posted!

[savan]

Thank you very much @thermokarst!!! It works right now!