taxonomic classification only at kingdom level-getting-ncbi-refseq-data

User Support
1

Hi
I'm facing an issue with taxonomic classification in QIIME 2. After running my sequences through the classifier, I only receive classifications at the kingdom level and no genus or species levels.

-ncbi-data \
    --p-query 33175[BioProject] \
    --o-sequences ncbi-refseqs-unfiltered.qza \
    --o-taxonomy ncbi-refseqs-taxonomy-unfiltered.qza

after this I followed

qiime rescript filter-seqs-length-by-taxon

qiime rescript filter-taxa

qiime rescript evaluate-fit-classifier

feature-classifier classify-sklearn


```
`qiime metadata tabulate ``
```
qiime taxa barplot
```

[taxonomy-3.tsv|attachment](upload://2hXgPEM8FEDPmTub3EQKmY7OIep.tsv) (144.6 KB)
[taxonomy-3.tsv|attachment](upload://2hXgPEM8FEDPmTub3EQKmY7OIep.tsv) (144.6 KB)
2

Hi @MSrinivasan,

If you search the forum you'll find that the most common reason for this is that your sequence data does not match the orientation of your classifier. For example see this post and the links therein for more details.

1 Like
3

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