Add taxonomy to biom file

[Zeina]

Hi all, I'm trying to add taxonomy to biom file, I run the command below.

> biom add-metadata -i 16s-feature-table.biom -o 16s-feature-FINAL-table.biom --observation-metadata-fp 16s-taxonomy.tsv --sc-separated taxonomy

I got this error, does anyone have any idea how to solve this problem? Thank you

Traceback (most recent call last):
  File "/softs/contrib/apps/anaconda/3/bin/biom", line 5, in <module>
    from biom.cli import cli
  File "/softs/contrib/apps/anaconda/3/lib/python3.8/site-packages/biom/__init__.py", line 51, in <module>
    from .table import Table
  File "/softs/contrib/apps/anaconda/3/lib/python3.8/site-packages/biom/table.py", line 195, in <module>
    from ._filter import _filter
  File "biom/_filter.pyx", line 1, in init biom._filter
ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject

Here an example of my 16s-taxonomy.tsv file

#OTUID	taxonomy	confidence
d50444f4bbe6bb5d66f6ebcb77bd7530	d__Bacteria;p__Patescibacteria;c__Gracilibacteria;o__Candidatus Peregrinibacteria;f__Candidatus Peregrinibacteria;g__Candidatus Peregrinibacteria;s__	0.743958950192406
9b58ed6668b7fe104cb5d0d66b300631	d__Bacteria;p__Chloroflexi;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__uncultured Anaerolineaceae bacteria;s__

[SoilRotifer (Mike Robeson)]

Hi @Zeina,

This does not directly address your question but.... If you'd like a simple and quick way to generate a QIIME 1 -like OTU / feature table using QIIME 2, I'd suggest this:

How to build an OTU table

Hi @neocat, This is intended. If you work through the tutorials again, you'll notice that the feature-table (i.e. the counts table) is kept as a separate file from the taxonomy. I suggest reading through the overview, for more details. If you'd like to take a quick look at an old-style QIIME 1 like table, you can run the following commands: qiime feature-table transpose \ --i-table table.qza \ --o-transposed-feature-table table-transposed.qza qiime metadata tabulate \ -…

One you have the visualization you can click to download the TSV file.

-Mike

[wasade (Daniel McDonald)]

Hi @Zeina,

It looks like there is an installation issue with biom, where a different version of numpy was installed into your environment than what biom was built against. Could you try running this from an unmodified QIIME 2 environment?

Best,
Daniel