[Bioperl-l] Failed to load module Bio::SeqIO::swiss

Chris Fields cjfields at illinois.edu
Thu Oct 21 11:05:17 EDT 2010


Like the error message says, you need to install Data::Stag (so, for some reason, this way left off).  However, I'm not sure why you are using fink as the version in stable is still 1.5.1; bioperl 1.6.1 is in fink-unstable.

chris

On Oct 21, 2010, at 3:45 AM, Chaogu Zheng wrote:

> I am extremely new to Bioperl and got a problem immediately after I
> installed it.
> 
> I installed Bioperl-pm5100 and Bioperl-run-pm5100 using fink.
> Everything seems to be fine. However, when I tried to retrieve some
> sequences from swissprot, I found the following errors.
> 
> It seems the module Bio::SeqIO::swiss can not be loaded, though I
> indeed found it under the correct directory. By the way, if I change
> 'swiss' to 'genbank' I can successfully run the program.
> 
> I don't know how to fix it. Anyone can help me?
> 
> 
> Ryan
> 
>>>>>>>>>>>>>>> 
> Bio::SeqIO: swiss cannot be found
> Exception
> ------------- EXCEPTION -------------
> MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/
> Stag.pm in @INC (@INC contains: /sw/lib/perl5/5.10.0/darwin-thread-
> multi-2level /sw/lib/perl5/5.10.0 /sw/lib/perl5/darwin-thread-
> multi-2level /sw/lib/perl5 /sw/lib/perl5/darwin /Library/Perl/Updates/
> 5.10.0/darwin-thread-multi-2level /Library/Perl/Updates/5.10.0 /System/
> Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/
> 5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/
> 5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /
> Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/
> Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/
> 5.10.0 .) at /sw/lib/perl5/5.10.0/Bio/Annotation/TagTree.pm line 123.
> BEGIN failed--compilation aborted at /sw/lib/perl5/5.10.0/Bio/
> Annotation/TagTree.pm line 123.
> Compilation failed in require at /sw/lib/perl5/5.10.0/Bio/SeqIO/
> swiss.pm line 208.
> BEGIN failed--compilation aborted at /sw/lib/perl5/5.10.0/Bio/SeqIO/
> swiss.pm line 208.
> Compilation failed in require at /sw/lib/perl5/5.10.0/Bio/Root/Root.pm
> line 439.
> 
> STACK Bio::Root::Root::_load_module /sw/lib/perl5/5.10.0/Bio/Root/
> Root.pm:441
> STACK (eval) /sw/lib/perl5/5.10.0/Bio/SeqIO.pm:570
> STACK Bio::SeqIO::_load_format_module /sw/lib/perl5/5.10.0/Bio/
> SeqIO.pm:569
> STACK Bio::SeqIO::new /sw/lib/perl5/5.10.0/Bio/SeqIO.pm:389
> STACK Bio::DB::WebDBSeqI::get_seq_stream /sw/lib/perl5/5.10.0/Bio/DB/
> WebDBSeqI.pm:472
> STACK Bio::DB::WebDBSeqI::get_Stream_by_acc /sw/lib/perl5/5.10.0/Bio/
> DB/WebDBSeqI.pm:314
> STACK Bio::DB::WebDBSeqI::get_Seq_by_acc /sw/lib/perl5/5.10.0/Bio/DB/
> WebDBSeqI.pm:186
> STACK Bio::Perl::get_sequence /sw/lib/perl5/5.10.0/Bio/Perl.pm:520
> STACK toplevel ./Documents/perl-programs/perl_test:8
> -------------------------------------
> 
> 
> For more information about the SeqIO system please see the SeqIO docs.
> This includes ways of checking for formats at compile time, not run
> time
> 
> ------------- EXCEPTION -------------
> MSG: acc P11217 does not exist
> STACK Bio::DB::WebDBSeqI::get_Seq_by_acc /sw/lib/perl5/5.10.0/Bio/DB/
> WebDBSeqI.pm:187
> STACK Bio::Perl::get_sequence /sw/lib/perl5/5.10.0/Bio/Perl.pm:520
> STACK toplevel ./Documents/perl-programs/perl_test:8
> -------------------------------------
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