I am trying to make local databases for the ncbi-blast+ package (version 2.60). I am doing so for 4 T-cell receptor genes. 3 of the 4 (TRAV, TRAJ, TRBV) have worked fine, but I am having problems with TRBJ. I say this because they should be the same format and if one works the rest works.
They take the format below:
>K02545|TRBJ1-1*01|Homo sapiens|F|J-REGION|749..796|48 nt|3| | | |15 AA|15+0=15| | | NTEAFFGQGTRLTVV
I used the following command (like I say, it was fine for the rest, oddly enough):
makeblastdb -in TRBJ_AA.fa -parse_seqids -dbtype prot
and I get the following error message:
BLAST options error: TRBJ_AA.fa does not match input format type, default input type is FASTA
One issue I checked was the length of the sequences being too short, but I believe 11 is the minimum length required (for inputs, don't know if that is the same for databases)- but would someone be able to confirm, that strikes me as the most likely candidate?
I'm happy to use some other metric, but I was hoping on keeping BLAST for consistency's sake for the time being.
edit: I know it's to late, but for reference I'm on Ubuntu 16.04.2 LTS x86_64 for all steps.