[Bioperl-l] Bio::Tools::Run::RepeatMasker crashes perl

John M.C. Ma manchunjohn-ma at uiowa.edu
Tue Jun 30 12:17:08 EDT 2009


Hi everyone,

(OS: OpenSuSE 11.1, Versions: Perl:v5.10.0-i586-linux-thread-multi,
Bioperl: 1.6.0-cpan, Bioperl-run: 1.6.1-cpan, Ensembl: Ver 54-cvs)

This is the first time I use Bio::Tools::Run::RepeatMasker, and it
came with a strange crash that I can't think of a reason. I would
rather think it's my problem?

My code involved pulling a sequence from Ensembl-variation, put it
into a PrimarySeq Object and run RepeatMasker on it:

use strict;
use warnings;
use Bio::SeqIO;
use Bio::PrimarySeq;
use Bio::Tools::Run::RepeatMasker;
use Bio::EnsEMBL::Registry;
use Bio::EnsEMBL::Variation::Variation;
[snips most Ensembl code as the sequence itself looks OK]
	my $ref_allele=$snp_obj->five_prime_flanking_seq.${$snp_obj->get_all_Alleles}[0]->allele.$snp_obj->three_prime_flanking_seq;
	my $mask_seq=Bio::PrimarySeq->new (-seq=>$ref_allele);
	my $rmasker_handle=Bio::Tools::Run::RepeatMasker->new(-species=>'rat',-noisy=>"1");
	my @masked_features=$rmasker_handle->run($mask_seq);
	my $masked_seq=$rmasker_handle->run;

And when I let the wrapper run, perl crashed with these warnings:

--------------------- WARNING ---------------------
MSG: RepeatMasker didn't find any repetitive sequences

---------------------------------------------------

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not open /tmp/EWLAmIVymd/wByClB8iqr.masked: No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw
/usr/lib/perl5/site_perl/5.10.0/Bio/Root/Root.pm:357
STACK: Bio::Root::IO::_initialize_io
/usr/lib/perl5/site_perl/5.10.0/Bio/Root/IO.pm:310
STACK: Bio::SeqIO::_initialize /usr/lib/perl5/site_perl/5.10.0/Bio/SeqIO.pm:450
STACK: Bio::SeqIO::fasta::_initialize
/usr/lib/perl5/site_perl/5.10.0/Bio/SeqIO/fasta.pm:81
STACK: Bio::SeqIO::new /usr/lib/perl5/site_perl/5.10.0/Bio/SeqIO.pm:347
STACK: Bio::SeqIO::new /usr/lib/perl5/site_perl/5.10.0/Bio/SeqIO.pm:373
STACK: Bio::Tools::Run::RepeatMasker::_run
/usr/lib/perl5/site_perl/5.10.0/Bio/Tools/Run/RepeatMasker.pm:320
STACK: Bio::Tools::Run::RepeatMasker::run
/usr/lib/perl5/site_perl/5.10.0/Bio/Tools/Run/RepeatMasker.pm:260
STACK: main::SeqList
/home/johnma/workspace/TaqMan_SNP_Order/TaqMan_SNP_Order.pl:40
STACK: /home/johnma/workspace/TaqMan_SNP_Order/TaqMan_SNP_Order.pl:63
-----------------------------------------------------------

What could happen?

Cheers,

John Ma,
University of Iowa


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