Qiime taxa filter-table error

thermokarst · April 30, 2018, 11:13pm

Hi @mly! Looks like you found a bug!

I opened a bug report up here: Handle whitespace in TSVTaxonomyFormat -> Metadata transformer · Issue #179 · qiime2/q2-types · GitHub

Okay, so in the meantime, here is a solution for you to move forward:

qiime tools export taxonomy.qza \
  --output-dir taxonomy-with-spaces
qiime metadata tabulate \
  --m-input-file taxonomy-with-spaces/taxonomy.tsv  \
  --o-visualization taxonomy-as-metadata.qzv
qiime tools export taxonomy-as-metadata.qzv \
  --output-dir taxonomy-as-metadata
qiime tools import \
  --type 'FeatureData[Taxonomy]' \
  --input-path taxonomy-as-metadata/metadata.tsv \
  --output-path taxonomy-without-spaces.qza

Okay, so that is a lot of steps (sorry!) but it should get you moving forward. Also, exporting will ruin the provenance tracking, so unfortunately you will lose out on that for the taxonomy artifact you are working with. Anyway, give that a shot and let us know how it goes! I just tested it locally and it worked as expected, by the way.

Thanks!