Why is this makeblastdb command not working? 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:

&gt;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.

Thank you.

edit: I know it's to late, but for reference I'm on Ubuntu 16.04.2 LTS x86_64 for all steps.
This looks like a bug in makeblastdb. Removing the final | | | from your sequence's description makes it work:

&gt;K02545|TRBJ1-1*01|Homo sapiens|F|J-REGION|749..796|48 nt|3| | | |15 AA|15+0=15


So does removing everything after the 1st space:

&gt;K02545|TRBJ1-1*01|Homo sapiens|F|J-REGION|749..796|48


There is nothing in the FASTA definition that would explain this and, even more weirdly, the presence of the | | | alone isn't enough to trigger the issue. I played around with this a little and it looks like it doesn't like the combination of + or -along with empty | |, but there's no clear pattern I can see:

These fail:

&gt;| | |15-| | |
&gt;| | |15+| | |
&gt;| | |15-1| | |
&gt;| | |15+1| | |


These work:

&gt;| |15+| |
&gt;| | |151| | |


So yeah, sounds like a bug. I suggest you report it to the NCBI devs. In the meantime, a simple fix would be to just keep the first space-separated field of your fasta header. Pass your fasta file through this:

awk '{print $1}' fasta.fa &gt; new.fa


That will print the 1st field of each line and, assuming you don't have spaces in your sequence, it should effectively sort this out for you.