standalone blast , database error

Question

[tcf.hcdg]

Hello

I would like to blast my sequences using NCBI standalone blast. I downloaded the lates version of blast(2.2.31+).

After downloading I extract the files and installed according to the instruction at the website. It was installed under C:\Program Files\NCBI\blast-2.2.31+

This folder contains the uninstaller, bin and doc. Then I downloaded the databases refseq_rna.00 and create a folder db within the installed blast.

C:\Program Files\NCBI\blast-2.2.31+\db

Then I configured my PCy creating the the environment variable "path" and giving the location of

C:\Program Files\NCBI\blast-2.2.31+\bin

Afterwords I opened the cmd from my system and to check whether the installation is ok I used the following commands.

Microsoft Windows [Version 6.1.7601]
Copyright (c) 2009 Microsoft Corporation. All rights reserved.

C:\Users\Ashar Hussain>cd /
C:\>cd Program Files/NCBI/blast-2.2.31+
C:\Program Files\NCBI\blast-2.2.31+>dir
 Volume in drive C has no label.
 Volume Serial Number is 40E5-5989

 Directory of C:\Program Files\NCBI\blast-2.2.31+

06/19/2015  10:06 AM    <DIR>          .
06/19/2015  10:06 AM    <DIR>          ..
06/18/2015  12:51 PM    <DIR>          bin
06/22/2015  12:27 PM    <DIR>          db
06/18/2015  12:51 PM    <DIR>          doc
06/19/2015  09:59 AM            62,465 Uninstall-ncbi-blast-2.2.31+.exe
               1 File(s)         62,465 bytes
               5 Dir(s)  228,627,599,360 bytes free

C:\Program Files\NCBI\blast-2.2.31+>cd bin
C:\Program Files\NCBI\blast-2.2.31+\bin>blastn -version
blastn: 2.2.31+
Package: blast 2.2.31, build Jun  2 2015 10:18:08
C:\Program Files\NCBI\blast-2.2.31+\bin>

Until this point this is working fine but when I want to check the databases I downloaded console is giving the messages like this

C:\Program Files\NCBI\blast-2.2.31+\bin>blastdbcmd -db refseq_rna.00 -info
BLAST Database error: No alias or index file found for nucleotide database [refs
eq_rna.00] in search path [C:\Program Files\NCBI\blast-2.2.31+\bin;;]

I tried to resolve the error by downloading the databases again but it didn't resolve.

Does anybody has idea? Any suggestions?

Thanks in advance

[GenoMax]

Did you download *all* "refseq_rna.NN" files and uncompress them? All file parts are needed to use the refseq_rna database and they all need to be in the same folder.

[tcf.hcdg]

Yes I downloaded all refseq_rna.(0-6) and uncompress them. All files are in same folder. But I keep the ".nal files" of all refseq_rna.NN in the same folder. Should I kept only one or all of them?

[GenoMax]

Great. Only one .nal file is needed. Do not include numbers at end of file names in your command. Try the following

blastdbcmd -db refseq_rna -info

[tcf.hcdg]

Still the same problem.

I save the blast and database in c/programme files(as mentioned in the question). IS this can be the problem?

[GenoMax]

I think the problem here is getting the paths correct (windows does not make this easy).

If your database files are in the C:\Program Files\NCBI\blast-2.2.31+\db directory and you are trying to run the blastdbcmd program from the C:\Program Files\NCBI\blast-2.2.31+\bin directory then let us see if the following works:

blastdbcmd -db C:\Program Files\NCBI\blast-2.2.31+\db\refseq_rna -info

Provide any error messages in full, if you see any.

[tcf.hcdg]

I think the problem is of path. this time I change the direction of database (s you mentioned) and the error is as follow:

Error: Too many positional arguments (1), the offending value: Files\NCBI\blast-2.2.31+\db\refseq_rna

C:\Program Files\NCBI\blast-2.2.31+>blastdbcmd -db C:\Program Files\NCBI\blast-2.2.31+\db\refseq_rna -info
USAGE
  blastdbcmd.exe [-h] [-help] [-db dbname] [-dbtype molecule_type]
    [-entry sequence_identifier] [-entry_batch input_file] [-pig PIG] [-info]
    [-range numbers] [-strand strand] [-mask_sequence_with mask_algo_id]
    [-out output_file] [-outfmt format] [-target_only] [-get_dups]
    [-line_length number] [-ctrl_a] [-show_blastdb_search_path]
    [-list directory] [-remove_redundant_dbs] [-recursive]
    [-list_outfmt format] [-exact_length] [-logfile File_Name] [-version]

DESCRIPTION
   BLAST database client, version 2.2.31+

Use '-help' to print detailed descriptions of command line arguments
========================================================================

Error: Too many positional arguments (1), the offending value: Files\NCBI\blast-2.2.31+\db\refseq_rna

[GenoMax]

Grr windows and spaces in names ... Try

blastdbcmd -db "C:\Program Files\NCBI\blast-2.2.31+\db\refseq_rna" -info

[tcf.hcdg]

Thanks alot. Now the problem has been solved. Spaces were the main problem.

Answer 1

[h.mon]

First, I would recommend you install Linux and do your bioinformatics stuff on it.

In case this seems too much trouble for a simple blast (and blast is all you want to do), do not use folders or files with spaces on its names. Never, ever. It will save you lots of troubles and headaches. So install Blast on something like C:\myProgs\blast, and keep your data on C:\Users\AsharHussain.

You may also create a blast.ini file to point Blast to your databases.

[tcf.hcdg]

Thanks a lot. Now the problem has been solved. Spaces were the main problem.

I tested this only for few sequences. But now I will install LINUX because I have large dataset.

[h.mon]

Although I strongly encourage you to install and learn Linux, you should consider first getting your blast results and then moving on to Linux. If your Windows is 64 bits and you file system is NTFS, it will be perfectly capable of dealing with large datasets.