Db was created without using the -parse_seqids option, but it was

sequenceserver
#1

I’m getting “ was created without using the -parse_seqids option of makeblastdb” reported upon startup on some of my databases. But, -parse_seqids WAS used.
Any ideas why this would happen?

#2

Hi Erya,

thanks for the message. Can you clarify which versions of BLAST and SequenceServer you’re using? The way BLAST does things has changed multiple times… so we find that sometimes its best to reformat from scratch.

Thanks!
Yannick

#3

I know this is an old post, but I am experiencing the same issue with SequenceServer (v3.1.3) using BLASTN 2.16.0+. Even when I run makeblastdb -parse_seqids manually, I still encounter the same error.

The FASTA download does not work correctly, and I receive the message that the database “was created without using the -parse_seqids option of makeblastdb.” As a result, I am unable to download the FASTA format.

Could you please advise on how to resolve this issue?

Thank you very much for your help.

#4

I did some debugging on my side and found that, in my case, the issue was related to the FASTA file name rather than the makeblastdb -parse_seqids option itself.Specifically, my FASTA files were named starting with square brackets, for example:

[gene]12345.fa

After renaming the files to avoid square brackets—using a format such as:

gene_12345.fa

the problem was resolved and FASTA download worked as expected.

I am not entirely sure of the underlying cause, but it may be related to how SequenceServer or BLAST handles file names or shell/glob expansion internally. Others encountering the same error may want to try renaming their FASTA files to exclude characters such as square brackets.

I hope this helps someone facing a similar issue.