[Bioperl-l] Re peatMasker not found

Smithies, Russell Russell.Smithies at agresearch.co.nz
Thu May 22 16:58:30 EDT 2008


Have you had tried RepeatMasker running on the command line?
If it doesn't run there, it's very unlikely to run through BioPerl.

Eg. 	/home/vdar/RepeatMasker/RepeatMasker  -species Ruminantia
-xsmall test.fa


--Russell

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-
> bio.org] On Behalf Of nisa_dar
> Sent: Friday, 23 May 2008 7:29 a.m.
> To: Bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] Re peatMasker not found
> 
> 
> 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
> >
> >
> 
> --
> View this message in context:
http://www.nabble.com/RepeatMasker-not-found-
> tp17218229p17411731.html
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
> 
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