blastn execution error, the correct command line format
1
0
Entering edit mode
6.4 years ago

so iam trying to test my blast+  standalone program with the following command

./blastn -db /home/Desktop/ncbi-blast-2.2.30+/db/nr  -query /home/Downloads/sequence.fasta  -out /home/CCMB/Downloads/output/result

but everytime i get the error not a valid output format

can anyone give me an idea of the general execution command and format for nucleotide blast and correct me if my command is miswritten

 

i tried the command

 ./blastn -db /home/Desktop/ncbi-blast-2.2.30+/db/nr -query /home/CCMB/Downloads/sequence.fasta -out /home/Downloads/outbox/result.txt

but it always shows the error
"BLAST Database error: No alias or index file found for nucleotide database [/home/Desktop/ncbi-blast-2.2.30+/db/nr] in search path [/home/Downloads/ncbi-blast-2.2.30+/bin::"

blast sequence nucleotide • 5.6k views
ADD COMMENT
3
Entering edit mode
6.4 years ago
edrezen ▴ 720

Hello,

You try to use blastn with the db bank being nr (protein bank), but blastn is made for comparing nucleotides bank vs another nucleotides bank.

So, you should use another db bank (like nt) or change to the correct blast tool (could be blastx in your case if your query bank has nucleotides)

Once your choice is made, you have to configure the db bank with the makeblastdb tool (look at this page). In your case, it should be something like this:

makeblastdb –in nr –dbtype prot 

or

makeblastdb –in nt –dbtype nucl

 

ADD COMMENT

Login before adding your answer.

Traffic: 2485 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6