[Bioperl-l] Re peatMasker not found

Smithies, Russell Russell.Smithies at agresearch.co.nz
Thu May 22 21:18:48 UTC 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
> >
> =============================================================
> ==========
> > Attention: The information contained in this message and/or
attachments
> > from AgResearch Limited is intended only for the persons or entities
> > to which it is addressed and may contain confidential and/or
privileged
> > material. Any review, retransmission, dissemination or other use of,
or
> > taking of any action in reliance upon, this information by persons
or
> > entities other than the intended recipients is prohibited by
AgResearch
> > Limited. If you have received this message in error, please notify
the
> > sender immediately.
> >
> =============================================================
> ==========
> >
> >
> 

=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================




More information about the Bioperl-l mailing list