Question: Blast-2.2.27+ Error
0
gravatar for wendy
6.7 years ago by
wendy0
wendy0 wrote:

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.

• 3.7k views
ADD COMMENTlink modified 6.7 years ago by Daniel3.7k • written 6.7 years ago by wendy0

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?

ADD REPLYlink written 6.7 years ago by Michael Dondrup46k

Thanks for your advise, it works now.

ADD REPLYlink written 6.7 years ago by wendy0
1
gravatar for vijay
6.7 years ago by
vijay1.5k
Chennai
vijay1.5k wrote:

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

ADD COMMENTlink written 6.7 years ago by vijay1.5k

Thank you very much,it's works!

ADD REPLYlink written 6.7 years ago by wendy0
0
gravatar for Daniel
6.7 years ago by
Daniel3.7k
Cardiff University
Daniel3.7k wrote:

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

ADD COMMENTlink written 6.7 years ago by Daniel3.7k

Thanks for your recommendation.

ADD REPLYlink written 6.7 years ago by wendy0
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