classification() unable to find NCBI accession number known to exist in database

[aubreyodom]

Session Info

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Hi there,

I'm finding that the classification() function is unable to pull information for various taxa from the NCBI nucleotide database as of late. As a toy example, take accession "NZ_LQBM01000006.1" (or "NZ_LQBM01000006"). This is present in the NCBI database as "Nesterenkonia jeotgali strain CD08_7 CD08_7_contig_6_consensus, whole genome shotgun sequence" but fails to return output with classification().

taxize::classification("NZ_LQBM01000006.1", db = "ncbi",
                       key = NULL,
                       max_tries = 3)

Which returns the output

══  1 queries  ═══════════════

Retrieving data for taxon 'NZ_LQBM01000006.1'

Not found. Consider checking the spelling or alternate classification
══  Results  ═════════════════

• Total: 1 
• Found: 0 
• Not Found: 0
No ENTREZ API key provided
 Get one via taxize::use_entrez()
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/
$NZ_LQBM01000006.1
[1] NA

attr(,"class")
[1] "classification"
attr(,"db")
[1] "ncbi"
Warning message:
Giving up on query after 3 tries. NAs will be returned. 

Any help or insight would be greatly appreciated. Thanks!

[zachary-foster]

The classification function takes taxon IDs or taxon names as input, so you need to convert your sequence accession number to a taxon ID like so:

taxize::classification(taxize::genbank2uid("NZ_LQBM01000006.1"), db = "ncbi")

[aubreyodom]

That resolves my issue - thank you!