[Bioperl-l] FeatureIO::gff.pm -- error fetching sofa.definition

[Tanya Gray]

Hi, I have a simple test script to read a GFF3 file using FeatureIO::gff.pm. Unfortunately it is throwing errors relating to retrieval of sofa.definition file:
MSG: failed to fetch http://umn.dl.sourceforge.net/sourceforge/song/sofa.definition, server threw 500

I am using Bioperl-1.5.0. I just wonder if anyone might know what the problem is.  Copy of the relevant script/ error messages below.

thank you
Tanya


relevant lines of script
---------------------------

my $file_features = "gff3.test";

my $fio = Bio::FeatureIO->new( -file =>$file_features, -format =>"GFF", -validate_terms=>0, -version=>3) or print "\nError occurred: " . $! ;


gff3.test
----------

##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123  .       gene    1000    9000    .       +       .       ID=gene00001;Name=EDEN

ERROR MESSAGES
---------------------
perl gff3test.pl                                                            [11:11]

-------------------- WARNING ---------------------
MSG: [1/5] tried to fetch http://umn.dl.sourceforge.net/sourceforge/song/sofa.definition, but server threw 500.  retrying...
---------------------------------------------------

-------------------- WARNING ---------------------
MSG: [2/5] tried to fetch http://umn.dl.sourceforge.net/sourceforge/song/sofa.definition, but server threw 500.  retrying...
---------------------------------------------------

-------------------- WARNING ---------------------
MSG: [3/5] tried to fetch http://umn.dl.sourceforge.net/sourceforge/song/sofa.definition, but server threw 500.  retrying...
---------------------------------------------------

-------------------- WARNING ---------------------
MSG: [4/5] tried to fetch http://umn.dl.sourceforge.net/sourceforge/song/sofa.definition, but server threw 500.  retrying...
---------------------------------------------------

-------------------- WARNING ---------------------
MSG: [5/5] tried to fetch http://umn.dl.sourceforge.net/sourceforge/song/sofa.definition, but server threw 500.  retrying...
---------------------------------------------------

------------- EXCEPTION  -------------
MSG: failed to fetch http://umn.dl.sourceforge.net/sourceforge/song/sofa.definition, server threw 500
STACK Bio::Root::IO::_initialize_io /usr/local/share/perl/5.8.7/Bio/Root/IO.pm:276
STACK Bio::Root::IO::new /usr/local/share/perl/5.8.7/Bio/Root/IO.pm:227
STACK Bio::OntologyIO::dagflat::defs_url /usr/local/share/perl/5.8.7/Bio/OntologyIO/dagflat.pm:361
STACK Bio::OntologyIO::dagflat::_initialize /usr/local/share/perl/5.8.7/Bio/OntologyIO/dagflat.pm:188
STACK Bio::OntologyIO::soflat::_initialize /usr/local/share/perl/5.8.7/Bio/OntologyIO/soflat.pm:145
STACK Bio::OntologyIO::new /usr/local/share/perl/5.8.7/Bio/OntologyIO.pm:169
STACK Bio::OntologyIO::new /usr/local/share/perl/5.8.7/Bio/OntologyIO.pm:178
STACK Bio::Ontology::OntologyStore::get_ontology /usr/local/share/perl/5.8.7/Bio/Ontology/OntologyStore.pm:225
STACK Bio::FeatureIO::gff::_initialize /usr/local/share/perl/5.8.7/Bio/FeatureIO/gff.pm:110
STACK Bio::FeatureIO::new /usr/local/share/perl/5.8.7/Bio/FeatureIO.pm:268
STACK Bio::FeatureIO::new /usr/local/share/perl/5.8.7/Bio/FeatureIO.pm:288
STACK toplevel gff3test.pl:15