Hi all I downloaded blast+ software package (for windows), and installed like the Bookshelf; to run it i used this
"ncbi-blast-2.2.25+/bin/blastn –query text_query.txt –db refseq_genomic –out output.txt"
but it didn't work and gave me an error:
"DESCRIPTION Nucleotide-Nucleotide BLAST 2.2.25+ Use '-help' to print detailed descriptions of command line arguments ======================================================================== Error: (106.18) NCBI C++ Exception: Error: (CArgException::eSynopsis) Too many positional arguments (1), the offending value: ûquery Error: (CArgException::eSynopsis) Application's initialization failed"
I couldn't what is my mistake. if possible help me (with more details please, because i am a bit freshman about bioinformatics). i really need it. thanks a lot in advance.
I tried it: you copy, pasted the command line from here: http://www.ncbi.nlm.nih.gov/books/NBK52637/
blastn –query text_query.txt –db refseq_rna –out output.txt
If I do this on a Mac I get the same error as you. So it is definitely the dash ('-'), this query looks the same as:
blastn -query text_query.txt -db refseq_rna -out output.txt Command line argument error: Argument "query". File is not accessible: `text_query.txt'
this is fine because I don't have that file! So it is definitely an encoding problem, UTF-8 versus ISO-latin I suppose.
Be wary about copy pasting commands.