I just downloaded a protein fasta file for Arabidopsis which I want to blast my data to. What I did is, I have put the fasta file in a folder, I have used the "makeblastdb" command:
Building a new DB, current time: 11/28/2018 11:21:43 New DB name: /mnt/d/Primula/Databases/Athaliana/GCF_000001735.4_TAIR10.1_protein New DB title: /mnt/d/Primula/Databases/Athaliana/GCF_000001735.4_TAIR10.1_protein.fasta Sequence type: Protein Keep Linkouts: T Keep MBits: T Maximum file size: 1000000000B Adding sequences from FASTA; added 48266 sequences in 2.25262 seconds.*
Both the fasta file and the resulting files are in the same folder. Now, this is my command line I use for the blast:
blastp -query /mypath/genomic.all.maker.proteins.fasta -out PrimVer_actinidia_Arabidopsis.blast.txt -db /pathtofastafolder/GCF_000001735.4_TAIR10.1_protein.fasta -evalue 1e-3 -outfmt 6*
I get this error:
"BLAST Database error: No alias or index file found for protein database"
I refer to the fasta in the -db command, so this is not the problem. Any insights on this?