Taxonomy import for SILVA majority_taxonomy_all_levels.txt

[Harry (Harry Batsang)]

Hi Thanks for sharing here.

I met a problem importing taxonomy files, it gives errors:

There was a problem importing majority_taxonomy_all_levels.txt:
majority_taxonomy_all_levels.txt is not a(n) TSVTaxonomyFormat file

Any idea to solve this failure?

Thanks a lot

[ebolyen (Evan Bolyen)]

For context, this was split off from 18S classifier using SILVA database and EMB primers which was just a very old topic.

Here’s the command that it looks like @Harry used (correct me if I’m wrong):

qiime tools import \
--type FeatureData[Taxonomy] \
--input-path SILVA_128_QIIME_release/taxonomy/18S_only/99/majority_taxonomy_all_levels.txt \
--output-path 18S_SILVA128_99_taxonomy.qza

[jairideout (Jai Ram Rideout)]

Hi @Harry! The taxonomy files included in SILVA_128_QIIME_release do not have headers. For example, here’s the first few lines from one of the majority_taxonomy_all_levels.txt files:

KC708424.1.1606 D_0__Eukaryota;D_1__Opisthokonta;D_2__Nucletmycea;D_3__Fungi;D_4__Incertae Sedis;D_5__Mucoromycotina;D_6__Incertae Sedis;D_7__Endogonales;D_8__Mucoromycotina sp. MIB 8855;D_9__;D_10__;D_11__;D_12__;D_13__;D_14__
GU338505.1.1724 D_0__Eukaryota;D_1__Opisthokonta;D_2__Holozoa;D_3__Metazoa (Animalia);D_4__Eumetazoa;D_5__Bilateria;D_6__Arthropoda;D_7__Chelicerata;D_8__Arachnida;D_9__Araneae;D_10__Macrargus alpinus;D_11__;D_12__;D_13__;D_14__
JQ271746.1.1978 D_0__Eukaryota;D_1__Amoebozoa;D_2__Discosea;D_3__Flabellinia;D_4__Vannellida;D_5__Platyamoeba;D_6__Vannella sp. LITHOV;D_7__;D_8__;D_9__;D_10__;D_11__;D_12__;D_13__;D_14__
...

Since the file is missing a header line, you’ll need to specify that the data is in HeaderlessTSVTaxonomyFormat. For example:

qiime tools import \
--type FeatureData[Taxonomy] \
--input-path SILVA_128_QIIME_release/taxonomy/18S_only/99/majority_taxonomy_all_levels.txt \
--output-path 18S_SILVA128_99_taxonomy.qza \
--source-format HeaderlessTSVTaxonomyFormat