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Blast-2.2.27+ Error

Hi everyone,

I am using Ubuntu 12.04 in VirtualBox to install ncbi-blast-2.2.27+ and I have downloaded the nucleotide database (nt.00.tar.gz - nt.12.tar.gz) from ftp://ftp.ncbi.nlm.nih.gov/blast/db.

When I try run the blastn by typing : blastn -db nt -query hbvref.fa, (the hbvref.fa is the sequence I obtained from Genbank) I got the following error:

****terminate called after throwing an instance of 'ncbi::CSeqDBException'**

**what():  NCBI C++ Exception:
"/am/ncbiapdata/release/blast/src/2.2.27/Linux32-Centos-icc/c++/ICC1010-ReleaseMT--Linux32-Centos-icc/../src/objtools/blast/seqdb_reader/seqdbatlas.cpp", line 152: Error: ncbi::SeqDB_ThrowException() - CSeqDBAtlas::MapMmap: While mapping file [/home/soklim/ncbi-blast-2.2.27+/db/nt.00.nsq] with 587556992 bytes allocated, caught exception:

NCBI C++ Exception:
"/am/ncbiapdata/release/blast/src/2.2.27/Linux32-Centos-icc/c++/ICC1010-ReleaseMT--Linux32-Centos-icc/../src/objtools/blast/seqdb_reader/seqdbatlas.cpp", line 152: Error: ncbi::SeqDB_ThrowException() - Validation failed: [end <= file_size] at /am/ncbiapdata/release/blast/src/2.2.27/Linux32-Centos-icc/c++/ICC1010-ReleaseMT--Linux32-Centos-icc/../src/objtools/blast/seqdb_reader/seqdbatlas.cpp:506**

**Aborted (core dumped)****

May I know what is the problem and how should I solve it?

Thank you very much.

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updated by Daniel Daniel • written by wendy • wendy

You should ask this question to ncbi support after making sure your blast db is complete and not truncated. Did you extract all the tar.gz files after downloading?

• 0 views • link
written by Michael Dondrup Michael Dondrup

Thanks for your advise, it works now.

• 0 views • link
written by wendy • wendy

2 answers

This error would occur if your database file is invalid(sometime the download may not be complete yet the process may stop). Also have you checked if the environment variables for BLAST are setup correctly. I think the files from ncbi contains database names like nt.11 nt.12 etc(until you have modified it), check out on this as well.

below link completely describes the CSeqDBException class!!!

http://www.ncbi.nlm.nih.gov/viewvc/v1/trunk/c%2B%2B/include/objtools/blast/seqdb_reader/seqdbcommon.hpp?revision=46889

• 0 views • link
written by vijay vijay

Thank you very much,it's works!

• 0 views • link
written by wendy • wendy

If you are starting out on linux and using virtual box I would highly recommend using Bio-Linux (http://nebc.nerc.ac.uk/tools/bio-linux) as it comes with all of the blast executables and environmentals set up (amongst everything else).

its ubuntu 12.04 as well now

• 2 views • link
written by Daniel Daniel

Thanks for your recommendation.

• 0 views • link
written by wendy • wendy

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