blast and update_blast.pl (nr files): No alias or index file found for protein database · Biostar

This is a test version of Biostars. For the public version, visit https://www.biostars.org.

blast and update_blast.pl (nr files): No alias or index file found for protein database

Good morning

I recently download the nr files from ncbi ftp using the update_blastdb.pl script. When I try to run blast, i got an error telling I need a nr.pl file. I just tried to use makeblastdb to create the file using (makeblastdb -dbtype prot -out nr -title "non-redundant") but the script doesn't seem to work. can anyone tell me how to index those files or where to find the nr.pl document?

blast update_blast.pl nr.pal index alais

• 2,573 views • link

written 8.6 years ago by paumarc •

Could you copy / paste the exact update_blastdb and blast commands, and the error message? Did you uncompressed the database after downloading?

• 0 views • link

written 8.6 years ago by h.mon

Hi, thanks for your quick reply

Fortunately, i could solve the problem. I just had some mistake in the paths

thanks

• 0 views • link

written 8.6 years ago by paumarc •

0 answers

No answers yet.

Log in to answer this question.

More posts like this

Create local Blast database alias with blastdb_aliastool fails
written 1.3 years ago by etienne •

After many many hours testing and searching on Internet, I can't make a database alias using the blastdb_aliastool. It starts with a very **un**documented NCBI …
How can I solve the database error?
written 4.4 years ago by Kenan.gk •

C:\Program Files\NCBI\blast-2.9.0+\bin>makeblastdb -in human.fasta -dbtype prot -out human Building a new DB, current time: 02/26/2022 20:02:21 New DB name: C:\Program Files\NCBI\blast-2.9.0+\bin\human New DB title: human.fasta …
I have a problem with blastx against database nr.
written 4.7 years ago by weimabri •

-Hello -I built the database for the nr with the following command $ makeblastdb -dbtype prot -in nr -which went well and generated .pal .psq …
how to run blastp against nr databse locally
written 6.2 years ago by Arora •

I have downloaded the preformatted nr db using the below command and uncompressed all files to a folder. The folder contains multiple files such as …
BLAST Database creation error
written 6.5 years ago by sahilbioinf0 •

I managed to download a nr ref sequence from ncbi ftp using the command.. wget 'ftp://ftp.ncbi.nlm.nih.gov/blast/db/nr.*.tar.gz' cat nr.*.tar.gz | tar -zxvi -f - -C . …
making nr database using makeblastdb
written 7.6 years ago by navela78

Hello, I am creating a local nr blast database using the following command makeblastdb -parse_seqids -dbtype 'prot' -in nr.fa -out nr -title nr -hash_index it …
creating a blast database
written 10.0 years ago by sukesh1411 •

Hi I downloaded the nr.gz file from blast ftp link. nr folder has 44 tar.gz files. I could not make a blast database using this …
Downloading Blast Database(nr)
written 10.1 years ago by Sumit •

Recently I have downloaded the nr database from ncbi website (ftp://ftp.ncbi.nlm.nih.gov/blast/db/). Although, in the readme file it is instructed that the pre-formatted database must be …
BLAST Database creation error
written 11.6 years ago by vigneshprbh37 •

Hey so for the past two days I have been trying to install and execute a stand alone blast named `ncbi-blast-2.2.30+` on a centos os …
Opening A Fasta File In Windows
written 14.4 years ago by Vivek •

<p>Hi all,</p> <p>I am a beginner with Blast+.I am using Windows.My aim as of now is to download the nr protein sequence in Fasta format …