Get.lineage, taxa not picked but do exist

I tried to use get.lineage to pick the taxa of interest (Eukaryota-Bacteria;Cyanobacteria) from SILVA_132_LSURef_tax_silva_trunc.fasta, and taxonomy file taxmap_slv_lsu_ref_132.txt, but the pick was only successful in the taxonomy file. I searched throughout the fasta file and there were these taxa. For example,

Hope I can get help here…

You cannot run get.lineage on the fasta file alone. The command only looks for the taxonomy information from the taxonomy file. If you give get.lineage both the taxonomy and fasta files, it will get the sequences that correspond to the desired taxonomy in the taxonomy file.


Hi Pat,
I did run the fasta and taxonomy files together: get.lineage(fasta=SILVA_132_LSURef_tax_silva_trunc.fasta, taxonomy=taxmap_slv_lsu_ref_132.txt, taxon=Eukaryota-Bacteria;Cyanobacteria)