[Bioperl-l] Re peatMasker not found

Smithies, Russell Russell.Smithies at agresearch.co.nz
Thu May 22 17:18:48 EDT 2008


AFAIK, you need to pay for Repbase (we pay around US$6,200 per year)
If you don't want to pay for Repbase, you'll need to create your own
repeat library.

--Russell

> -----Original Message-----
> From: vdar at yorku.ca [mailto:vdar at yorku.ca]
> Sent: Friday, 23 May 2008 9:14 a.m.
> To: Smithies, Russell
> Cc: Bioperl-l at lists.open-bio.org
> Subject: RE: [Bioperl-l] Re peatMasker not found
> 
> I have tried it and it gives the following message
> 
> RepeatMasker could not find the repeat library at:
>     /home/vdar/RepeatMasker/Libraries/RepeatMasker.lib
>  or
>     /home/vdar/RepeatMasker/Libraries/RepeatMaskerLib.embl
> Please download the latest RepeatMasker library from
> http://www.girinst.org and install before using RepeatMasker
> 
> 
> I've downloaded and installed censor-4.2 from www.girinst.org already
but of no
> use. I have seen that RepeatMasker/Libraries/RepeatMasker.lib is
empty. What
> should I do?
> 
> 
> 
> Quoting "Smithies, Russell" <Russell.Smithies at agresearch.co.nz>:
> 
> > 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.
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
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