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

Chaogu Zheng cgzheng86 at gmail.com
Thu Oct 21 04:45:40 EDT 2010


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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