Question: BLAST-2.6.0+ error: No alias or index file found for nucleotide database
0
gravatar for z.zangishei
2.4 years ago by
z.zangishei0 wrote:

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.

blast software error • 2.6k views
ADD COMMENTlink modified 2.4 years ago by Biostar ♦♦ 20 • written 2.4 years ago by z.zangishei0
2

use the name of your makeblastdb output;

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

not

 -db C:\Users\ZZ\Desktop\blastdb\OrAe.fasta
ADD REPLYlink written 2.4 years ago by Pierre Lindenbaum121k
1

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.

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by genomax69k

how did you "create the blast database " ?

ADD REPLYlink written 2.4 years ago by Pierre Lindenbaum121k

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!

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by z.zangishei0

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.

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by z.zangishei0

what are the files available under:

 C:\Users\ZZ\Desktop\blastdb\
ADD REPLYlink written 2.4 years ago by Pierre Lindenbaum121k

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.

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by z.zangishei0
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