Question: Error Using Makeblastdb
1
gravatar for Uncle Gabby
7.7 years ago by
Uncle Gabby20
Uncle Gabby20 wrote:

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$
makeblastdb database blast • 4.3k views
ADD COMMENTlink modified 6.1 years ago by Biostar ♦♦ 20 • written 7.7 years ago by Uncle Gabby20
5
gravatar for norlingjr
7.7 years ago by
norlingjr80
norlingjr80 wrote:

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.)

ADD COMMENTlink modified 7.7 years ago • written 7.7 years ago by norlingjr80

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.

ADD REPLYlink written 7.7 years ago by Uncle Gabby20

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

ADD REPLYlink written 7.7 years ago by norlingjr80

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.

ADD REPLYlink modified 7.7 years ago • written 7.7 years ago by Rm8.0k

TY. I got it to work too.

ADD REPLYlink written 7.7 years ago by Uncle Gabby20

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

ADD REPLYlink written 7.7 years ago by Uncle Gabby20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1063 users visited in the last hour