Here is the command I used:
blastdbcmd -entry_batch input.gi.txt -out file.out -target_only -outfmt %t -db my_protein_database.fasta
I got an error "Error: Entry not found in BLAST database". I have the indexed my database and .phr, .pin, .prj etc files (created by vmatch)are in the same directory where my protein database (my_protein_database.fasta) is but the blastdbcmd is in the user/bin directory. I am a bit suspicious about the index files as it was created by vmatch. I was wondering if there is any other way to build the protein database index using blast function that can be compatible for blastdbcmd. Any suggestions to point out where exacty I'm wrong?
i'm using blastdbcmd: 2.2.25+ version.