Why is this makeblastdb command not working?
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.