3.3 years ago by
The "blastdbcmd" will not run blastx. For that, use the blastx command. I'm not sure what your goal is but do you really want to run blastx, or blastp of the corresponding protein (NP_000113.1) against nr?
From the accession you are entering, it looks like you may be using the wrong database. This is RefSeq human mRNA accession, which seems very unlikely to be present in the standard nr protein database. Table 3b here shows pre-formatted nucleotide databases that include human NM accessions, like human_genomic_transcript.tar.gz.
To confirm what OIDs are present in your nr database, you can use the blastdbcmd -entry all -outfmt '%o' options.