Barrnap to QIIME2 to PiCRUST

Trying to run PiCRUST as a quick pass to explore diversity within 60+ samples after QIIME2 (imported FASTA to QZA, assigned taxonomy, converted QZA to table). Currently my exported taxonomy table (tsv) will not allow me to run picrust2, is there a way to export the taxonomy table as a QZA needed for the picrust2 command?

Below is the picrust command I had been trying:

module load qiime2/2019.10
qiime picrust2 full-pipeline
–i-table taxonomy.tsv
–i-seq QZA/D0606M02_assembly_bac.qza
–output-dir D0606M02_bac
–p-threads 20
–p-hsp-method pic
–p-max-nsti 2
–verbose

and resulting with:
(1/1) Invalid value for “–i-table”:
‘taxonomy.tsv’ is not a QIIME 2 Artifact (.qza)

If anyone has been able to use this pipeline or have any alternatives, I would greatly appreciate it! Thank you in advance.

-Rachel

Hi @rweisend,

To clarify, did you have a taxonomy.qza and then export it to a taxonomy.tsv? If so, you should be able to simply pass in taxonomy.qza as is.

What steps did you take to produce the “exported table?” It sounds like you may need to import that .tsv table into the appropriate format using qiime tools import. You can see which formats of input data are importable with the following command: qiime tools import --show-importable-formats. Please see the importing tutorial for more details and don’t hesitate to follow up if you need more details :smiley: .

Hi @andrewsanchez, thank you for your help!

I tried using the QZA that I had used to create the TSV file, when I ran that it resulted with this error:

(1/1) Invalid value for “–i-table”: Expected an artifact of at least type FeatureTable[Frequency]. An artifact of type FeatureData[Sequence] was provided.

The following is how I created the TSV file:
module load qiime2/2020.2
qiime tools export
–input-path D0606M02_bac_taxa.qza
–output-path exported-feature-table/D0606M02_bac

This results in a TSV. I was looking for how to convert this into the necessary qza artifact. Any suggestions?

Thanks again for the help.
Best,
Rachel

Hi @rweisend,

The error message you shared says that instead of passing in an FeatureTable[Frequency] artifact, you passed in FeatureData[Sequence].

From the section on semantic types in the QIIME 2 docs we know that FeatureTable[Frequency] is “a feature table (e.g., samples by OTUs) where each value indicates the frequency of an OTU in the corresponding sample expressed as raw counts.” FeatureData[Sequence] is “a single unaligned sequence associated with a feature identifier (e.g. a representative sequence).”

The first question I have for you is, are you surprised that the artifact you passed in to --i-table was a FeatureData[Sequence]? It sounds to me like this is not the taxonomic information you thought it was.

Secondly, the q2-picrust2 tutorial, says:

The required inputs are --i-table and --i-seq , which need to correspond to QIIME2 artifacts of types FeatureTable[Frequency] and FeatureData[Sequence], respectively.

So you need to pass in FeatureTable[Frequency], not taxonomic information.

I hope that helps! Let us know if you need more help.

Cheers,

Hi Andrew,

Thank you for the clarification, I am in fact having trouble creating that FeatureTable[Frequency] from qiime. When I previously made my table it was in the format of a TSV and therefore not able to be used for the PiCRUST command.

What would be the best method for creating the FeatureTable[Frequency]?

Thanks again for your help.

Best,
Rachel

There are important reasons why I don’t think that’s quite right. I’m not sure what you are referring to when you said, “When I previously made my table.” Are you referring to the export step? The export step did not produce a feature table. None of the commands you shared above created a feature table (in any format, .tsv or otherwise) or referenced a feature table. While the .tsv was not in the appropriate format (a .tsv instead of a q2 artifact), more importantly it did not contain the appropriate data either, as I shared above:

You can’t get from a taxonomy in a .tsv to a feature table. If you haven’t already, I highly recommend working through these tutorials to understand ways by which you can produce a feature table:

Hope that helps - good luck!

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