Hello,
I have been trying the last days to make my database for blast work but I really don't know how to figure out this problem.
Begining from the start of the problem, I want to make a blastp against a protein database that I have created.
Here is an example of my sequence identifiers and how they are formatted:
>TRA_G345655|locus=scaffold45|99209|101155|-|translate_table|standard
I try to make the blast database with the following command:
makeblastdb -in database.fa -title database -dbtype prot -out protdb -parse_seqids
It does not work and it gives me the following error:
No volumes were created because no sequences were found.
BLAST Database creation error: Defline lacks a proper ID around line 1
When I try it without '-parse_seqids', it works fine and it generated the three files with pin, psq and phr.
I put these 3 files with my database.fa fasta file in one folder called DB and then I try to run blastp with the following command:
blastp -query query.fa -db DB -out proteins_blastp_1e-30_table.txt -evalue 1e-30 -outfmt 6
or with:
blastp -query query.fa -db DB/database.fa -out proteins_blastp_1e-30_table.txt -evalue 1e-30 -outfmt 6
or with:
blastp -query query.fa -db database -out proteins_blastp_1e-30_table.txt -evalue 1e-30 -outfmt 6
But it gives me the following error:
BLAST Database error: No alias or index file found for protein database [database] in search path
How can I solve this problem or where is the origin of this problem?
The scenario you are describing can never happen, blastp would never ask for a nucleotide database, so you first need to get the association between commands and error message right. Most likely that you simply mixed up the blast programs (blastp/blastn/x)
No, I have not mixed up blastp/blastn/x. This is the simply the situation I am describing, I have two fasta files of proteins and I want to use blastp and this is the error I get which I have copied from my linux shell.I ran the command again, I updated the error, it must have been a mistake with nucleotide.
Yes you have, but you have also updated your question with a new error message, because in the first version it was saying :"No alias or index file found for nucleotide database" now it says protein.
Hey can you give me some advice on a blast installation matter?
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 systemi managed to download a nr ref sequence from ncbi ftp using the command
and extracted the file using the command
I got an nr file of 33 gb size
but when I try to format the file using the command
I get the error showing
Can you give any suggestions on the nature of the problem and how I can solve it?
Thanks