Issue importing TSV Taxonomy file

[mitchso (Mitch Syberg-Olsen)]

Hi,

I am trying to import a manually generated taxonomy file into qiime2 and receiving the following error:

There was a problem importing taxonomy_table.txt:
    taxonomy_table.txt is not a(n) HeaderlessTSVTaxonomyFormat file

I am using qiime2 version 2017.10 on an Ubuntu server with the following command:

qiime tools import --type 'FeatureData[Taxonomy]' --source-format HeaderlessTSVTaxonomyFormat --inputpath /path/taxonomy_table.txt --output-path /path/taxonomy_table.qza

Previously, this has worked perfectly for me when importing taxonomy files from Silva (release 128), for example:

qiime tools import --type 'FeatureData[Taxonomy]' --source-format HeaderlessTSVTaxonomyFormat --inputpath /path/silva128/97/majority_taxonomy_all_levels.txt --output-path /path/silva128/97/97_majority_taxonomy_all_levels.qza

I believe it must be something to do with the formatting of the text file I have generated however I just can't seem to pick out any differences in formatting between the two files.

The format for both should follow:

[Accession number][space][Taxonomic assignment][new line]

Here is an clip of the silva file, which has worked for me:

GU194623.1.1603	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__Opiliones;D_10__Compsidolon salicellum;D_11__;D_12__;D_13__;D_14__
KP730482.1.1626	D_0__Eukaryota;D_1__Opisthokonta;D_2__Holozoa;D_3__Metazoa (Animalia);D_4__Eumetazoa;D_5__Bilateria;D_6__Platyhelminthes;D_7__Rhabditophora;D_8__Macrostomida;Ambiguous_taxa;D_10__;D_11__;D_12__;D_13__;D_14__
LN827620.1.1554	D_0__Eukaryota;D_1__Opisthokonta;D_2__Holozoa;D_3__Metazoa (Animalia);D_4__Eumetazoa;D_5__Bilateria;D_6__Nematoda;D_7__Chromadorea;D_8__Rhabditida;Ambiguous_taxa;D_10__;D_11__;D_12__;D_13__;D_14__

And here is a clip of my own file:

KJ759545.1 D_0__Eukaryota;D_1__SAR;D_2__Alveolata;D_3__Ciliophora;D_4__SAL;D_5__Intramacronucleata;D_6__Sprirotrichea;D_7__Oligotrichia;D_8__Strombidiida;D_9__Tontoniidae;D_10__Tontoniidae
KJ762332.1 D_0__Eukaryota;D_1__SAR;D_2__Alveolata;D_3__Ciliophora;D_4__SAL;D_5__Intramacronucleata;D_6__Spirotrichea;D_7__Oligotrichia;D_8__Strombidiida;D_9__Strombidiida;D_10__Strombidiida
KJ761781.1 D_0__Eukaryota;D_1__SAR;D_2__Alveolata;D_3__Ciliophora;D_4__SAL;D_5__Intramacronucleata;D_6__Spirotrichea;D_7__Oligotrichia;D_8__Strombidiida;D_9__SPIOL1;D_10__SPIOL1

The only discernable difference I can pick out is the extra number tailing the accession in the silva file, but that is just the length of the nucleotide sequence in the related fasta file so I do not see why that would prevent me from importing my file into qiime2.

I feel like there must be something hiding in plain sight that I am missing but I can't figure it out.
I have attached my file below.
Any help would be greatly appreciated!

Thanks in advance

taxonomy_table.txt (33.7 KB)

[jairideout (Jai Ram Rideout)]

Hi @mitchso! The taxonomy files need to be in TSV format, meaning that a tab character should separate the Accession number from the Taxonomic assignment instead of a space:

[Accession number][tab][Taxonomic assignment][new line]

Give that a shot and let us know if it works for you!

[mitchso (Mitch Syberg-Olsen)]

Hi Jai,

I have updated the formatting of the file and it works beautifully Thanks a lot!
In case someone else runs in to this issue, the working file now looks like:

KJ759545.1      D_0__Eukaryota;D_1__SAR;D_2__Alveolata;D_3__Ciliophora;D_4__SAL;D_5__Intramacronucleata;D_6__Sprirotrichea;D_7__Oligotrichia;D_8__Strombidiida;D_9__Tontoniidae;D_10__Tontoniidae
KJ762332.1      D_0__Eukaryota;D_1__SAR;D_2__Alveolata;D_3__Ciliophora;D_4__SAL;D_5__Intramacronucleata;D_6__Spirotrichea;D_7__Oligotrichia;D_8__Strombidiida;D_9__Strombidiida;D_10__Strombidiida
KJ761781.1      D_0__Eukaryota;D_1__SAR;D_2__Alveolata;D_3__Ciliophora;D_4__SAL;D_5__Intramacronucleata;D_6__Spirotrichea;D_7__Oligotrichia;D_8__Strombidiida;D_9__SPIOL1;D_10__SPIOL1