I am trying to use taxonomizr in R to get taxonomy from a csv file with NCBI accession numbers.
However, using these lines:
bacterial<-read.csv('unique_accession.csv') taxaId<-accessionToTaxa("bacterial$Accession_Number","accessionTaxa.sql") getTaxonomy(taxaId,taxaNodes,taxaNames)
I followed taxonomizr vignette in correctly setting it up. I've tested it by giving just accession numbers, and it has been able to give taxonomic classifications.
But when I provide it with my csv file, instead of getting taxonomic classifications for all my accession numbers, I am getting NA in the classification.
I was wondering if anyone else has run into this issue, and how to solve it.