Hi, I'm trying to do an rpsblast using ncbi-blast-2.5.0+. I have a file containing gi numbers as my query and my command line is below.
rpsblast -query t -db results/Cog/Cog -out rps-blast.out -evalue 1e-2 -outfmt 6
Oddly the rpbslast keeps giving me this error:
Warning: [rpsblast] Error initializing remote BLAST database data loader: Protein BLAST database 'Cog/Cog nr' does not exist in the NCBI servers
My query file (t) looks like this. I've tried to remove search using just the numbers (292833481) but it still doesn't solve the problem. gi|292833481 gi|383341230 gi|289693981
However, when I try to the same search but using a fasta file as query, it runs fine and gives the results I need.
rpsblast -query GCF_000005845.2_ASM584v2_protein.faa -db results/Cog/Cog -out rps-blast.out -evalue 1e-2 -outfmt 6
Is there something that I did wrong here? What is the correct way to format query a list of gi's for blast? Thanks!