Question: Need help to solve Standalone blast error
0
gravatar for ashokkumar.mb
11 months ago by
ashokkumar.mb0 wrote:

Hi

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 • 292 views
ADD COMMENTlink modified 11 months ago by Asaf7.6k • written 11 months ago by ashokkumar.mb0
1

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 11 months ago • written 11 months ago by genomax83k

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 11 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 11 months ago by genomax83k
0
gravatar for Asaf
11 months ago by
Asaf7.6k
Israel
Asaf7.6k wrote:

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

ADD COMMENTlink written 11 months ago by Asaf7.6k
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