Is Makeblastdb Creat 3 Files Like Formatdb + Blast Error

Question

[Sara]

Hi everyone,

I have a big problem!

I install blast+ for windows.

I run this :

makeblastdb.exe -in filename.fasta -dbtype nucl -out filename_BLASTdb

apparently it create db coz I have this message:

a -dbtype nucl -out 020_GC.LD_ED_19July_BLASTdb


Building a new DB, current time: 07/20/2011 09:47:50
New DB name:   020_GC.LD_ED_19July_BLASTdb
New DB title:  020_GC.LD_ED_19July.fasta
Sequence type: Nucleotide
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1073741824B
Adding sequences from FASTA; added 809 sequences in 0.289397 seconds.

right?

but there is no file created so when i try to blast

blastn.exe     -db filename_BLASTdb -word_size 7 -query mature.fasta -out filename.blastsmallRNA     -evalue 10

there is an error i can not understand:

Error: (106.18)
NCBI C++ Exception:
    Error: (CArgException::eSynopsis) Too many positional arguments (1), the off
ending value: filename.fasta-db
    Error: (CArgException::eSynopsis) Application's initialization failed

could you please help

thanks

[Sara]

Thanks DAN for your answer . you are right i correct "-" problem but there is another error

blastn -query mature.fasta -db 020_GC.LD_ED_19July_BLASTdb -out outfile.txt

Command line argument error: Argument "out". File is not accessible:  `outfile.txt'

what does it mean? it should put the result in this outfile , shouldn't?

Many thanks

[Michael Schubert]

Please don't ask a follow-up question by answering. Either edit your original question (if it's something minor) or open up a new one. Thanks!

Answer 1

[DG]

Is it possible you did a copy/paste of the commands somewhere and there is a character encoding issue? This question seems quite similar to yours:

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

The error you are getting isn't the error you expect to get because it can't find the file, it is a problem parsing your command line input (too many positional arguments).

[Sara]

Thanks DAN for your answer . you are right i correct `-` problem but there is another error

blastn -query mature.fasta -db 020_GC.LD_ED_19July_BLASTdb -out outfile.txt
Command line argument error: Argument "out". File is not accessible:  `outfile.txt'

what does it mean? it should put the result in this outfile , shouldn't?

Many thanks

[DG]

In all likelihood it is a permissions problem that prevents writing to a file in that directory? Or the filename already exists and you don't have permission to overwrite it? Something like that would be my guess.

[Sara]

can i change the permission of a directory and to write there?

[Michael Schubert]

You can use chmod for that on a *nix shell. Google is your friend to find some examples ;)

[Michael Schubert]

Oh scratch that, you're on Windows. Easiest way would be to supply the the full path to a directory you have writing permissions.