Question: Need help to solve Standalone blast error
gravatar for ashokkumar.mb
3 months ago by
ashokkumar.mb0 wrote:


I am trying run standalone blastn for some of contigs from genome assembly. So i have installed ncbi-blast-2.9.0+ version and downloaded nr database, and then extracted all 43 files. Then tried blastn command, but it says BLAST database error: No alias or index file found for nucleotide database. Please help me to solve this error. Should I index all extracted database files ? or just extraction of all file is fine ?

database error • 117 views
ADD COMMENTlink modified 3 months ago by Asaf6.2k • written 3 months ago by ashokkumar.mb0

Not sure what version of the indexes you downloaded (v5 or older) but there should be more than 43 files for nr (there are 115 in v5). Sounds like you did not download the complete dataset.

ADD REPLYlink modified 3 months ago • written 3 months ago by genomax71k

Can you please send me the link where we can download nr database. because the page from which I have downloaded has only 43 files. all started with nr_v5.00.tar.gz to nr_v5.43.tar.gz.

ADD REPLYlink written 3 months ago by ashokkumar.mb0

I just checked on NCBI's FTP site and there seem to be 43 files. In the past sometimes there has been an incomplete copy of databases on NCBI's FTP site so I suggest you send a ticket in to their helpdesk. It may take 2-3 business days to hear back from them but they do respond.

ADD REPLYlink written 12 weeks ago by genomax71k
gravatar for Asaf
3 months ago by
Asaf6.2k wrote:

nr is protein database, nt is nucleotides. Try using blastp or blastx if the input is DNA

ADD COMMENTlink written 3 months ago by Asaf6.2k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2023 users visited in the last hour