error message unknow argument : " query_gencode" on local_bast_client.pl command on ubuntu
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.
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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/
Actually I'm using the cgview comparative tool, but this script doesn't work :
if you are aligning protein data to a nucleotide database, there is no
-query_gencodeparameter to apply, onlydb_gencodebecause 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.