Question: BLAST Database error: No alias or index file found for nucleotide database
3
gravatar for arronslacey
4.1 years ago by
arronslacey230
United Kingdom
arronslacey230 wrote:

Hi - I am trying to run blastn, and then also SIFT standalone. I am having database configuration issues however as I am getting the following:

 

 

arron@arron-Ideapad-Z570 ~/Phd/programs/sift4.0.3b $ blastn -query test/lacI.fasta -db db/swissprot/
BLAST Database error: No alias or index file found for nucleotide database [db/swissprot/] in search path [/home/arron/Phd/programs/sift4.0.3b:::]

 

After some advice from other threads, I downloaded a protein database, for example swissprot:

 

wget ftp://ftp.ebi.ac.uk/pub/databases/fastafiles/uniprot/uniprotkb_swissprot.gz

zcat uniprotkb_swissprot.gz | awk '{if (/^>/) { print ">" $2} else { print $_}}' > swissprot.fa

 

 

and then used makeblastdb to create a blast database:

 

arron@arron-Ideapad-Z570 ~/Phd/programs/sift4.0.3b/db/swissprot $ makeblastdb -in swissprot.fa -dbtype prot

Building a new DB, current time: 10/27/2014 13:18:57
New DB name:   swissprot.fa
New DB title:  swissprot.fa
Sequence type: Protein
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1073741824B
Adding sequences from FASTA; added 546439 sequences in 19.0039 seconds.

 

 

yet I am still getting the same problem. What am I doing wrong?

blastn blast sift makeblastdb • 28k views
ADD COMMENTlink modified 2.5 years ago by mforthman30 • written 4.1 years ago by arronslacey230
6
gravatar for RamRS
4.1 years ago by
RamRS19k
Houston, TX
RamRS19k wrote:

Once you create the database using makeblastdb, your database name is swissprot.fa

Your command should be:

blastn -query test/lacI.fasta -db <path_to_db>/swissprot.fa

I'd recommend using a custom name with makeblastdb that you can then supply to the -db parameter - that should avoid confusion with existing file-names.

 

ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by RamRS19k
1

hi RamRS - I actually think I should have been using blastp as swissprot as a protein database...yes it works fine with blastp

ADD REPLYlink written 4.1 years ago by arronslacey230
1

It would seem I have run out of coffee once again - should've seen that bit from a mile away. Or probably because it's Monday. 

Anyway, glad you found the solution :-)

ADD REPLYlink written 4.1 years ago by RamRS19k
1

This was actually very helpful for me. Thank you!! (Even though you were missing out on coffee). 

ADD REPLYlink written 3.5 years ago by thorerges60
1

Oh well, another coffee-less Monday, another shot in the dark!

ADD REPLYlink written 3.5 years ago by RamRS19k
0
gravatar for mforthman
2.5 years ago by
mforthman30
mforthman30 wrote:

I'm experiencing a similar issue.

Using a set of genomes/transcriptomes, I invoked makeblastdb as follows:

makeblastdb -in exons_for_blastall.fasta -input_type fasta -dbtype nucl \
-title exons_for_blastall -parse_seqids -out exons_for_blastall

This is what is reported on screen:

Building a new DB, current time: 06/01/2016 21:31:34
New DB name:   exons_for_blastall
New DB title:  exons_for_blastall
Sequence type: Nucleotide
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 231417 sequences in 52.605 seconds.

Next, I tried to blastn this db with the .fasta file I used to generate it (all vs. all blast):

blastn -db exons_for_blastall -query exons_for_blastall.fasta -perc_identity 80\
 -out exons_for_blastall.blasted -evalue 1e-20

You'll see I used the db name exactly. This resulted in the same error message that started this thread. Interestingly, makeblastdb created a number of files, for which I have no idea what they are for: .nhr, .nin, .nog, .nsd, .nsi, and .nsq.

ADD COMMENTlink modified 2.5 years ago by RamRS19k • written 2.5 years ago by mforthman30

I am not sure why people always choose the same name as their fasta file as the basename for the database.

Are all the ".n" files in the same directory? Could you try to create a new db in a different directory with a different name and see if that helps.

ADD REPLYlink written 2.5 years ago by genomax59k

Figure out the problem. For some reason, blastn doesn't like spaces in paths to a file, even if the appropriate symbol to indicate a space in a directory name is used.

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by mforthman30
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