Error Using Makeblastdb

Question

[Uncle Gabby]

Hi there,

I am trying to run makebastdb to create a new BLAST database. The program starts but cuts out abruptly with an Error:

Error: ncbi::s_FixBioseqDeltas() - Bioseq must have Seq-data or Delta containing only literals.

The input should be good. They are correctly formatted fasta files I pulled from Entrez.

The complete output is pasted below. I would appreciate any help or insight anyone can offer. Thank you!

$ makeblastdb -in Herpesviridae.fna -dbtype nucl -out Herpesviridae.db
Building a new DB, current time: 09/20/2012 14:15:59
New DB name:   Herpesviridae.db
New DB title:  Herpesviridae.fna
Sequence type: Nucleotide
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B

volume: Herpesviridae.db

file: Herpesviridae.db.nin
file: Herpesviridae.db.nhr
file: Herpesviridae.db.nsq

Error: NCBI C++ Exception:
    "/am/ncbiapdata/release/blast/src/2.2.27/IntelMAC-universal/c++/GCC401-ReleaseMT--IntelMAC-universal/../src/objtools/blast/seqdb_writer/build_db.cpp", line 407: Error: ncbi::s_FixBioseqDeltas() - Bioseq must have Seq-data or Delta containing only literals.

Walters-MacBook-Pro:NCBI Data walternmoss$

Answer 1

[norlingjr]

I'm not sure, but from the error message "Bioseq must have Seq-data or Delta containing only literals." I would check the .fna-file for non-literal characters, mainly "*" and "-".

What do you get if you run this?

$ grep -oE "[\*\-]" Herpesviridae.fna | wc -l

If this is not zero, you may need to re-download your sequences. Otherwise, is there any way to share your sequence file so I can try it?

update

in a few places in your file (50 to be exact) there are entries like

<?xml version="1.0" encoding="UTF-8"?>

<eFetchResult>
    <ERROR>Unable to obtain query #1</ERROR>
</eFetchResult>

I think you may need to recreate your file. (You could try removing these entries and creating the database, but your results might lack these lost sequences.)

[Uncle Gabby]

Thank you I found 374 dashes, all in the title sections. I think the sequence data are good. I am posting a link to my file on dropbox: http://dl.dropbox.com/u/104729694/Herpesviridae.fna Thank you for helping me troubleshoot this.

[norlingjr]

Thanks! I get exactly the same error - so nothing wrong with your installation! checking if I can find a solution.

[Rm]

As mentioned above: After deleting the all the junck lines "starting with ?xml..." and checked the formating it works:

makeblastdb -in Herpesviridae.fna -dbtype nucl -out Herpesviridae.db

Building a new DB, current time: 09/20/2012 15:11:59 New DB name: Herpesviridae.db New DB title: Herpesviridae.fna Sequence type: Nucleotide Keep Linkouts: T Keep MBits: T Maximum file size: 1073741824B Adding sequences from FASTA; added 6000 sequences in 0.774491 seconds.

[Uncle Gabby]

TY. I got it to work too.

[Uncle Gabby]

I got rid of that junk and makeblastdb worked fine. Thanks! I can't believe I missed those errors.