Question: Command line BLAST
0
gravatar for shrinivas.mchavan
14 months ago by
shrinivas.mchavan0 wrote:

I installed command line BLAST and then added pre-formatted database from NCBI. now i am trying to validate it. When I extract a entry from database, it is shown in fasta format in command prompt. I want to export that file in text format. To this end, i am using following command-

C:\Program Files\NCBI\blast-2.7.1+>blastdbcmd.exe -db refseq_rna.00 -entry nm_000122 -outfmt %f -out Test_query

but then there pops up a Command line argument error: Argument "out". File is not accessible: `Test_query'. How can I resolve it? I would appreciate your help.

output sequence • 746 views
ADD COMMENTlink modified 14 months ago • written 14 months ago by shrinivas.mchavan0
1

Isn't it a permission error? try 'C:\Program Files\NCBI\blast-2.7.1+\blastdbcmd.exe' -db 'C:\Program Files\NCBI\blast-2.7.1+\refseq_rna.00' ......

At your home directory.

ADD REPLYlink written 14 months ago by fishgolden370

Nope it isn't. Tried your suggestion. Following error pops up-

Error: Too many positional arguments (1), the offending value: files\NCBI\blast-2.7.1+\refseq_rna.00' Error: (CArgException::eSynopsis) Too many positional arguments (1), the offending value: files\NCBI\blast-2.7.1+\refseq_rna.00'

ADD REPLYlink written 14 months ago by shrinivas.mchavan0

Ok, then change the path of the output file.(please ignore my first comment)

C:\Program Files\NCBI\blast-2.7.1+>blastdbcmd.exe -db refseq_rna.00 -entry nm_000122 -outfmt %f -out C:\User\<your user name>\Test_query
ADD REPLYlink modified 14 months ago • written 14 months ago by fishgolden370

Didn't work. Following error appears- Error: Too many positional arguments (1), the offending value: 1\test_query Error: (CArgException::eSynopsis) Too many positional arguments (1), the offending value: 1\test_query

ADD REPLYlink written 14 months ago by shrinivas.mchavan0

Ok, how about using double quotation

C:\Program Files\NCBI\blast-2.7.1+>blastdbcmd.exe -db refseq_rna.00 -entry nm_000122 -outfmt %f -out "C:\User\<your user name>\Test_query"

My first comment may work with double quotation marks, too.

ADD REPLYlink modified 14 months ago • written 14 months ago by fishgolden370

Nope it isn't. Tried your suggestion. Following error pops up-

Error: Too many positional arguments (1), the offending value: files\NCBI\blast-2.7.1+\refseq_rna.00' Error: (CArgException::eSynopsis) Too many positional arguments (1), the offending value: files\NCBI\blast-2.7.1+\refseq_rna.00'

ADD REPLYlink written 14 months ago by shrinivas.mchavan0

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

ADD REPLYlink written 14 months ago by genomax65k

Ok. I will be careful.

ADD REPLYlink written 14 months ago by shrinivas.mchavan0

This is probably not related to your issue but you should not use the refseq_rna.00 as db identifier. This refseq_rna is most likely a blastdb formatted in several subparts, so it is better to use simple refseq_rna (omit the .<number>) . you will see there is a refseq_rna.pal file which is in fact the 'main file' of your blastDB.

Apart from that : have you tried putting quotes around the %f thing? Linux will not stumbled over it but perhaps windows will?

ADD REPLYlink written 14 months ago by lieven.sterck4.5k

my first guess would otherwise also be the permission issue . Can you create any kind of file in the directory where you want to put that 'Test_query' file?

ADD REPLYlink written 14 months ago by lieven.sterck4.5k
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