BLAST-2.6.0+ error: No alias or index file found for nucleotide database

Question

[z.zangishei]

Hi all- I just started to use blast with blast-2.6.0+. When I create the blast database and try to run blastn through the following command line:

C:\Users\ZZ\Desktop\blast-2.6.0+\bin\blastn.exe -query C:\Users\ZZ\Desktop\blastdb\sly.fasta -db C:\Users\ZZ\Desktop\blastdb\OrAe.fasta -out C:\Users\ZZ\Desktop\blastdb\output

the following error displayed:

BLAST Database error: No alias or index file found for nucleotide database [C:\Users\ZZ\Desktop\blastdb\OrAe.fasta] in search path [C:\Users\ZZ;C:\Users\ZZ\Desktop\blastdb;]

What am I doing wrong? (if possible help me with more details please). Thanks a lot in advance.

[Pierre Lindenbaum]

use the name of your makeblastdb output;

 -db C:\Users\ZZ\Desktop\blastdb\OrAe

not

 -db C:\Users\ZZ\Desktop\blastdb\OrAe.fasta

[GenoMax]

As @Pierre hinted, what you did wrong is you appear to have not created the blast database index to search against using something like makeblastdb -dbtype nucl -in your_fasta.fa -out name_for_database. This needs to be done as a separate, one-time step.

[Pierre Lindenbaum]

how did you "create the blast database " ?

[z.zangishei]

I have created blast database first as following command:

C:\Users\ZZ\Desktop\blast-2.6.0+\bin\makeblastdb.exe -in C:\Users\ZZ\Desktop\blastdb\OrAe.fasta -out C:\Users\ZZ\Desktop\blastdb\OrAe -dbtype 'nucl' -hash_index

and following result was displayed:

Building a new DB: current time 02/20/2017 15:46:57 New DB name: C:\Users\ZZ\Desktop\blastdb\OrAe New DB title: C:\Users\ZZ\Desktop\blastdb\OrAe.fasta Sequence type: Nucleotide Keep MBits: T Maximum file size: 1000000000B Adding sequence from FASTA: added 72042 sequences in 8.24439 seconds.

C:\Users\ZZ>_

also, all OrAe.nhd, OrAe.nhi, OrAe.nhr, OrAe.nin, OrAe.nog, OrAe.nsd, OrAe.nsi, and OrAe.nsq files have been appeared in the same C:\Users\ZZ\Desktop\blastdb directory, but when run blastn as previous post the "No alias or index file found for nucleotide database" error is diplayed!

[z.zangishei]

Thanks Pierre, I tried as you said. It seems the program is running as there is no any error! I will inform the final result as soon it would be done.

[Pierre Lindenbaum]

what are the files available under:

 C:\Users\ZZ\Desktop\blastdb\

[z.zangishei]

OrAe.fasta (as subject) and sly.fasta (as query) together with all OrAe.nhd, OrAe.nhi, OrAe.nhr, OrAe.nin, OrAe.nog, OrAe.nsd, OrAe.nsi, and OrAe.nsq. Ofcourse, both suffix-less files output and OrAe appeared after awhile.