error message unknow argument : " query_gencode" on local_bast_client.pl command on ubuntu

Question

[Maloki]

I'am using local_blast_client.pl command to create local blast file, but when I run the command

perl local_blast_client.pl -i test_input_protein.fasta -o blast_rs.txt -b blastn -d myDB I get this error message.

DESCRIPTION Nucleotide-Nucleotide BLAST 2.6.0+

Use '-help' to print detailed descriptions of command line arguments

Error: Unknown argument: "query_gencode" Error: (CArgException::eInvalidArg) Unknown argument: "query_gencode" Program failed, try executing the command manually. Open blast_rs.txt to view the BLAST results.

[JC]

where do you get that perl script? You can directly run tblastn with the proper configuration, here is the documentation https://www.ncbi.nlm.nih.gov/books/NBK279684/

[Maloki]

Actually I'm using the cgview comparative tool, but this script doesn't work :

perl local_blast_client.pl -i test_input_protein.fasta -o blast_rs.txt -b blastn -d myDB

[JC]

if you are aligning protein data to a nucleotide database, there is no -query_gencode parameter to apply, only db_gencode because your query is already in protein space and you can translate your db according to a specific genetic code.

I guess the program you are trying to use needs nucleotide as the input query.