An Error By Using Ncbi-Blast-2.2.25+ (On Windows)

Question

[Mohammad Reza Bakhtiarizadeh]

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.

regards

[Michael]

might be an encoding problem: '-query' vs. 'ûquery', did you copy paste that command line (eg. from a pdf?) If so, try to re-type it completely yourself. Otherwise it could be a bug.

[Pierre Lindenbaum]

what's the content of "text_query.txt" ?

[Mohammad Reza Bakhtiarizadeh]

text_query.txt is a set of EST sequences that i want to blast them.

Answer 1

[Michael]

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.

[Mohammad Reza Bakhtiarizadeh]

Thanks so much for your useful answer. you are right. i fixed it. and another question please? how can i get just the first hit for each sequence? i don't know what code i write to do this. thanks again for your favor.

regards

[Michael]

For your additional question look here.

[Reyhaneh]

Hi everyone, I had the same problem and by retyping it was solved. Now my problem is that I am using C~ process to send the same command and it seems like it is basically copying and pasting and I get the same error when I use it through c# (but not through the run when I type it). Any idea how I can solve it? Thanks.

[Reyhaneh]

Hi everyone, I had the same problem and by retyping it was solved. Now my problem is that I am using C# process to send the same command and it seems like it is basically copying and pasting and I get the same error when I use it through c# (but not through the run when I type it). Any idea how I can solve it? Thanks.

Answer 2

[shaileenmcgovern]

Hi there, I know this has been answered, but I was finding the same issue even after retyping the "-" manually. I changed tack and replaced the "-out outfile.outfileExtension" argument to " > outfile.outfileExtension" and it worked. I then had to run another blast and tried the "-out" and then it worked?! It might be useful for someone out there!