Problem importing taxonomy.tsv file


I manually created a taxonomy file in excel and saved as tab seperated .txt format it looks like this

OTU ReferenceTaxon

New.ReferenceOTU65 k__Bacteria; p__Actinobacteria; c__Rubrobacteria; o__Rubrobacterales; f__Rubrobacteraceae; g__Rubrobacter; s__
203418 k__Bacteria; p__Actinobacteria; c__Thermoleophilia; o__Solirubrobacterales; f__Solirubrobacteraceae; g__; s__
New.CleanUp.ReferenceOTU7255 k__Bacteria; p__Chloroflexi; c__Thermomicrobia; o__JG30-KF-CM45; f__; g__; s__
New.CleanUp.ReferenceOTU6111 k__Bacteria; p__Actinobacteria; c__Nitriliruptoria; o__Nitriliruptorales; f__Nitriliruptoraceae; g__; s__
1126886 k__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; o__Rhizobiales; f__Bradyrhizobiaceae; g__Balneimonas; s__
248468 k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales; f__Micromonosporaceae; g__; s__

I tried a couple of variants of this command but had no luck :frowning:

qiime tools import
–input-path taxonomy.txt
–output-path taxonomy.qza
–type ‘FeatureData[Taxonomy]’

Would you be able to help me out with this ?

Many thanks in advance.


Hi @Sean_K_Bay,

What happens if you remove the header (the line with “OTU ReferenceTaxon”) and issue:

$ qiime tools import --input-path taxonomy.txt \
    --output-path taxonomy.qza \
    --type FeatureData[Taxonomy] \
    --source-format HeaderlessTSVTaxonomyFormat

My guess is the header is presenting some challenges. By removing the header, and explicitly telling QIIME the format of the input file, I was able to get the taxonomy data pasted in the thread to load.

Happy new year!



This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.