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?
I'm experiencing a similar issue.
Using a set of genomes/transcriptomes, I invoked makeblastdb as follows:
This is what is reported on screen:
Next, I tried to blastn this db with the .fasta file I used to generate it (all vs. all blast):
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.
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.
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.
Hello! I'm trying to parse the database UNITE to BLAST and I am getting this same error, but actually, not all .n files are generating (just the .nhr, .nin, .nsq).
This is the command I am using:
Is there something missing?
Please open a new question and reference this post in there. Do not add answers unless you're answering the top-level question.
I had this error but fixed it by first "cd"-ing (changing directory) to the actual database-containing directory and then running the blastdbcmd command.