Question: error message unknow argument : " query_gencode" on command on ubuntu
gravatar for Maloki
6 days ago by
Maloki10 wrote:

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

perl -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.

sequence • 53 views
ADD COMMENTlink written 6 days ago by Maloki10

where do you get that perl script? You can directly run tblastn with the proper configuration, here is the documentation

ADD REPLYlink written 6 days ago by JC9.6k

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

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

ADD REPLYlink written 5 days ago by Maloki10

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.

ADD REPLYlink written 1 day ago by JC9.6k
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