Error launching sequenceserver after making new BLAST database

Hi, I’m encountering an error launching sequenceserver after making a new BLAST database with the command ‘makeblastdb’ in Terminal. I get the following error message:

" Error obtaining BLAST databases.

Tried: blastdbcmd -recursive -list /Users/donaldnclarke/Documents/BlastDBs -list_outfmt “%f %t %p %n %l %d”


BLAST Database error: Error: Not a valid version 4 database."

I haven’t had an issue with this before, and have made multiple DBs, last one ~6 months ago. I’m wondering whether it is an issue with the input fasta file I’m using to make the DB, or if it might be something with the version of BLAST or sequenceserver I have?

Has anyone encountered this before? I’d appreciate any suggestions for fixing this!

Default BLAST database version since BLAST-2.10 is dbV5 [1, 2].

“Not a valid version 4 database” error likely means that the database was made with a latest version of the BLAST but the SequenceServer running is pointed to a version of BLAST earlier than the version 2.10. I have checked this by trying to open a recently made index with an earlier version of BLAST, i.e. 2.6.0.
[1] BLAST+ 2.10.0 now available with improved composition-based statistics - NCBI Insights
[2] Protein BLASTDBs are accession-based - NCBI Insights

1 Like

Dear @clarken and @uludag,

Yes, with NCBI’s many changes in BLAST database format, there is no trivial way to keep everything working in all circumstances. To make it simple, I would do the following:

  • if you’re using old databases, use old BLAST and old sequenceserver (1.0)
  • if you want newer things (newer BLAST and SequenceServer 2.0), ensure that you’re using the newer database formats. The “easiest” can be to reformat them from FASTA.

Kind regards,


Lab - Supergene adaptive introgression - Improving bee health - Haplodiploid - Cloud BLAST servers