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
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.
Then I configured my PCy creating the the environment variable "path" and giving the location of
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
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.
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?
Great. Only one .nal file is needed. Do not include numbers at end of file names in your command. Try the following
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?
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:
Provide any error messages in full, if you see any.
I think the problem is of path. this time I change the direction of database (s you mentioned) and the error is as follow:
Grr windows and spaces in names ... Try
Thanks alot. Now the problem has been solved. Spaces were the main problem.