[Bioperl-l] Help me to deal with "MSG: blastall call crashed: -1blastall ..."

[Joseph Bedell]

Hi-

This is only a guess, but by the looks of the error statement (the -d
/ecoli1.nt), I think you need to set an environment variable to point to
the location of your ecoli1.nt database. I believe that you can set
either $BLASTDATADIR or $BLASTDB to the correct directory and it should
work.

Joey


>-----Original Message-----
>From: bioperl-l-bounces at portal.open-bio.org [mailto:bioperl-l-
>bounces at portal.open-bio.org] On Behalf Of hcuong
>Sent: Friday, October 24, 2003 10:20 PM
>To: bioperl-l at bioperl.org
>Subject: [Bioperl-l] Help me to deal with "MSG: blastall call crashed:
-
>1blastall ..."
>
>Hi, Please help me. I try to make BLAST search for the first time by
the
>test script:
>> #----------------
>>
>> #!/usr/bin/perl
>>
>>  use strict;
>>
>> use Bio::Tools::Run::StandAloneBlast;
>>
>>  my @params = (program => 'blastn',
>>
>>                             database => 'ecoli1.nt');
>>
>> my $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
>>
>> my $input = Bio::Seq->new(-id => "test query",
>>
>>                                              -seq => "ACTAAGTGGGGG");
>>
>> my $blast_report = $factory->blastall ($input);
>>
>>  print "$blast_report\n";
>>
>> #----------------
>
>But I always get the following error only:
>
>>  ------------- EXCEPTION  -------------
>>
>> MSG: blastall call crashed: -1 blastall -p  blastn  -d  /ecoli1.nt
-i
>/tmp/bSh3ZAfK7n  -o  /tmp/gv9wpcMj8g
>>
>>  STACK Bio::Tools::Run::StandAloneBlast::_runblast
/usr/local/ActivePerl-
>5.6/lib/site_perl/5.6.1/Bio/Tools/Run/StandAloneBlast.pm:633
>>
>> STACK Bio::Tools::Run::StandAloneBlast::_generic_local_blast
>/usr/local/ActivePerl-
>5.6/lib/site_perl/5.6.1/Bio/Tools/Run/StandAloneBlast.pm:602
>>
>> STACK Bio::Tools::Run::StandAloneBlast::blastall
/usr/local/ActivePerl-
>5.6/lib/site_perl/5.6.1/Bio/Tools/Run/StandAloneBlast.pm:489
>>
>> TACK toplevel blast_local.pl:15
>
>
>---
>Nguyen Huu Cuong
>Plant Cell Biotechnology Department
>Institute of Biotechnology, NCST
>18 Hoang Quoc Viet, Cau Giay, Ha Noi
>Tel: 84 - 4 - 7562368
>Email: hcuong at ibt.ac.vn