Importing greengenes headerless taxonomy file

[duderostome (Matthew Rogers)]

I’m having a problem with the --source-format argument when importing a Greengenes headerless tsv into an artifact.

qiime tools import --type ‘FeatureData[Taxonomy]’ --input-path 97_otu_taxonomy.txt --source-format HeaderlessTSVTaxonomyFormat --output-path 97_otu_taxonomy.qza

Error: no such option: --source-format

I’d be grateful for any suggestions. My goal is to run closed OTU picking on the dada generated OTUs to run PICRUST on my data.

I’m running QIIME 2 release 2018.8 and Python 3.5.5, with all plugins matching this release.

System versions
Python version: 3.5.5
QIIME 2 release: 2018.8
QIIME 2 version: 2018.8.0
q2cli version: 2018.8.0

[Mehrbod_Estaki]

Hi @duderostome,

I believe your issue is just regarding the new changes in 2018.8 release.
As of the 2018.8 q2 release, the --source-format is replaced with --input-format , so replacing this should fix your problem.

[duderostome (Matthew Rogers)]

Perfect, runs great now. Thanks Mehrbod.