error retrieving sequence

Hi, I’ve have a problem retrieving sequences from the Sequenceserver results. I get the same message with all of my databases so I don’t think it’s a fasta header issue. The error message reports the path it tried to access as having a comma:

"ERROR: incorrect number of sequences found.

Dear user,

We have found less sequence than expected.

This is likely due to a problem with how databases are formatted. Please share this text with the person managing this website so they can resolve the issue.

You requested 1 sequence with the following identifiers: AFLA_071800, from the following databases: /usr/local/bin/ncbi-blast-2.2.30, /db/AFLA_only.fasta. But we found 0 sequence."

Is it possible that is the issue?


Very weird that location of BLAST+ binary is listed here.

Looks like you are using SequenceServer 0.8.7 from the gem install.

Can you post me the output of:
blastdbcmd -db /db/AFLA_only.fasta -entry AFLA_071800

Is this a problem with BLAST+ 2.2.29 and lesser as well?

– Priyam

Yes, I tried with BLAST+ 2.2.28 and got the same error.

This is what I get with blastdbcmd:

blastdbcmd -db /db/AFLA_only.fasta -entry AFLA_071800
BLAST Database error: No alias or index file found for nucleotide database [/db/AFLA_only.fasta] in search path [/home/brian:/usr/local/bin/ncbi-blast-2.2.30+/db:]

I was able to get the sequence retrieval to work by moving my BLAST databases to my home directory. I previously had them in /usr/local/bin/ncbi-blast-2.2.30+/db. I had changed the permissions using sudo chmod -R a+rwx $BLASTDB so I thought it wasn’t a permissions issue, but there must have been some issue with the location.

Thanks for your help.


I’m glad you were able to resolve it.

– Priyam