Blast-2.2.27+ Error

Question

[wendy]

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.

[Michael]

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?

[wendy]

Thanks for your advise, it works now.

Answer 1

[vijay]

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

[wendy]

Thank you very much,it's works!

Answer 2

[Daniel]

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

[wendy]

Thanks for your recommendation.