Problem importing taxonomy.tsv file

[Sean_K_Bay (Sean Bay)]

Hi

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

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.

Cheers,
Sean

[wasade (Daniel McDonald)]

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!

Best,
Daniel