[Bioperl-l] Re peatMasker not found

nisa_dar vdar at yorku.ca
Thu May 22 15:28:50 EDT 2008


Finally I have put my whole code inside the Directory RepeatMasker and now
this error message comes

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Repeat Masker Call(RepeatMasker  -noint -mam /tmp/uZzDGdH78C/oyiUOrQOer
2> /dev/null 1>/dev/null) crashed: 32512

STACK: Error::throw
STACK: Bio::Root::Root::throw
/opt/rocks/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:328
STACK: Bio::Tools::Run::RepeatMasker::_run
/opt/rocks/lib/perl5/site_perl/5.8.8/Bio/Tools/Run/RepeatMasker.pm:266
STACK: Bio::Tools::Run::RepeatMasker::run
/opt/rocks/lib/perl5/site_perl/5.8.8/Bio/Tools/Run/RepeatMasker.pm:220
STACK: try.pl:28
-----------------------------------------------------------


Here is my code

#!/usr/bin/perl

use strict;
use warnings;

use Bio::Seq;
use Bio::Tools::Run::StandAloneBlast;
use Bio::Search::Hit::HitI;
use Bio::Search::Hit::BlastHit;
use Bio::Search::HSP::BlastHSP;
use Bio::Search::HSP::HSPI;
use Bio::SearchIO;
use Bio::Tools::Run::RepeatMasker;

BEGIN {

        $ENV{REPEATMASKERDIR} = '/home/vdar/RepeatMasker';

 }


my @params = ("mam" => 1,"noint"=>1);
my $factory = Bio::Tools::Run::RepeatMasker->new(@params);
my $in  = Bio::SeqIO->new(-file => "boechera.fasta", -format => 'fasta');
  my $seq = $in->next_seq();
#
  #return an array of Bio::SeqFeature::FeaturePair objects
  my @feats = $factory->run($seq);
#
#  # or
#
#  $factory->run($seq);
#  my @feats = $factory->repeat_features;
#
#  #return the masked sequence, a Bio::SeqI object
  my $masked_seq = $factory->run;
#  
  if ($masked_seq){
        print "yes\n";
#  
  }


Does anyone know what does that mean and what to do now? bcs I have seen
that RepeatMasker program resides in this directory and I didn't get the
previous message this time that program not found.

Thanks!









Sendu Bala-2 wrote:
> 
> nisa_dar wrote:
>> please see my full message and all the approaches that i have been doing
>> to
>> tell my pogram where repeat masker is...what else is correct if these are
>> not?
> 
> We don't know where you installed RepeatMasker. Only you do. You need to 
> supply that installation directory to $ENV{REPEATMASKERDIR} in your code.
> 
> 
>> Sendu Bala-2 wrote:
>>> nisa_dar wrote:
>>>> ok now I have installed repeat masker, with its prerequisites as given
>>>> on 
>>>> http://www.repeatmasker.org/
>>>> but now I am getting this error message. 
>>>>
>>>> RepeatMasker program not found as  or not executable. 
>>>>
>>>> what should I do?
>>> Well now you have to correct your code to tell it where you installed 
>>> RepeatMasker:
>>>
>>>
>>>>> On May 13, 2008, at 1:59 PM, nisa_dar wrote:
>>> [...]
>>>>>> BEGIN {
>>>>>>
>>>>>> 	$ENV{REPEATMASKERDIR} =
>>>>>> '/opt/rocks/lib/perl5/site_perl/5.8.8/Bio/Tools/';
>>>>>>
>>>>>>  }
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

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