Question: Is Makeblastdb Creat 3 Files Like Formatdb + Blast Error
0
gravatar for Sara
8.0 years ago by
Sara130
Sara130 wrote:

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

makeblastdb blast • 6.6k views
ADD COMMENTlink written 8.0 years ago by Sara130
2
gravatar for Dan Gaston
8.0 years ago by
Dan Gaston7.1k
Canada
Dan Gaston7.1k wrote:

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).

ADD COMMENTlink written 8.0 years ago by Dan Gaston7.1k

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

ADD REPLYlink written 8.0 years ago by Sara130

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.

ADD REPLYlink written 8.0 years ago by Dan Gaston7.1k

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

ADD REPLYlink written 8.0 years ago by Sara130

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

ADD REPLYlink written 8.0 years ago by Michael Schubert6.9k

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

ADD REPLYlink written 8.0 years ago by Michael Schubert6.9k
0
gravatar for Sara
8.0 years ago by
Sara130
Sara130 wrote:

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

ADD COMMENTlink written 8.0 years ago by Sara130

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!

ADD REPLYlink written 8.0 years ago by Michael Schubert6.9k
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