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
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).
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
You can use chmod for that on a *nix shell. Google is your friend to find some examples ;)
Oh scratch that, you're on Windows. Easiest way would be to supply the the full path to a directory you have writing permissions.
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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
what does it mean? it should put the result in this outfile , shouldn't?
Many thanks
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!