[Bioperl-l] [GUSDEV] Another error executing ISF
Alberto M. R. Dávila
davila at fiocruz.br
Fri Jan 27 00:05:35 UTC 2006
Dear Chris,
Happy 2006 !
I am not sure about the exact record the ISF plugin was trying to
read/parse, but I think it is the first one, anyway I am listing the first
5 GIs of our file for your testing:
85539529
56130985
54300415
54288810
50604596
The whole file is really big (1.4GB) as it contains all the nucleotide
sequences of "kinetoplastida [organism]" from genbank in genbank format.
Hope you can catch "the bug" ;-)
Kindest regards, Alberto
>
> Sorry for the uninformative error message.
>
> The unflattener uses a collection of heuristics to infer a canonical
> gene-mRNA-CDS-exon feature hierarchy from a flattened genbank style
> file. Due to the highly variable nature of some genbank records this
> isn't always possible, and some data massaging is required beforehand.
> I don't know what the context of this message is, but I presume you're
> aware of this from the docs.
>
> The only time I've seen this before was with the genbank submission of
> the pombe genome, which has some very.. unusual features purportedly of
> type mRNA; the actual gene models are encoded using 'gene' and 'CDS'
> features. This confuses the heuristics a little. The only way I've been
> able to deal with this one was to manually remove the mRNA features
> (they appeared to be just fragments and not actual gene models) using
> $unf->remove_types(['mRNA']) beforehand.
>
> Can you send the accession of the record you're trying this on (or
> email me the file off-list if it isn't too large). I'll try and get a
> more informative error message in there.
>
> On Jan 26, 2006, at 10:19 AM, Ricardo Balbi wrote:
>
>> Hi all,
>>
>> Anybody could help me with this error ?
>>
>> thanks in advance,
>> Ricardo
>>
>> 2006/1/26, Aaron J. Mackey <amackey at pcbi.upenn.edu>:
>>>
>>>
>>> This is a BioPerl "Unflattener" error; it's unable to automatically
>>> reconstruct the gene/mRNA/exon logic of some (or all) of the
>>> annotation in your genbank file. To get help with this, you should
>>> post a message to the BioPerl mailing list (bioperl-l at bioperl.org),
>>> including a snippet of your genbank file.
>>>
>>> -Aaron
>>>
>>> On Jan 26, 2006, at 11:53 AM, Ricardo Balbi wrote:
>>>
>>>> Hi all,
>>>>
>>>> After making some changes in the gus mapping file to ignore some
>>>> features of the kinetoplastida database, I followed in the
>>>> execution of the ISF, however without success.
>>>>
>>>> Somebody could help me with this error?
>>>>
>>>> thanks in advance,
>>>> Ricardo
>>>>
>>>> ERROR:
>>>>
>>>> ------------- EXCEPTION -------------
>>>> MSG: structure_type 2 is currently unknown
>>>> STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq /usr/local/
>>>> bioperl15/Bio/SeqFeature/Tools/Unflattener.pm:1419
>>>> STACK GUS::Supported::Plugin::InsertSequenceFeatures::unflatten /
>>>> GUS/gus_home/lib/perl/GUS/Supported/Plugin/
>>>> InsertSequenceFeatures.pm:353
>>>> STACK
>>>> GUS::Supported::Plugin::InsertSequenceFeatures::processFeatureTrees
>>>> /G
>>>> US/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm:
>>>> 720
>>>> STACK GUS::Supported::Plugin::InsertSequenceFeatures::run /GUS/
>>>> gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm:330
>>>> STACK (eval) /GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm:
>>>> 549
>>>> STACK GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport /GUS/
>>>> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm:541
>>>> STACK GUS::PluginMgr::GusApplication::doMajorMode_Run /GUS/gus_home/
>>>> lib/perl/GUS/PluginMgr/GusApplication.pm:459
>>>> STACK GUS::PluginMgr::GusApplication::doMajorMode /GUS/gus_home/lib/
>>>> perl/GUS/PluginMgr/GusApplication.pm:357
>>>> STACK GUS::PluginMgr::GusApplication::parseAndRun /GUS/gus_home/lib/
>>>> perl/GUS/PluginMgr/GusApplication.pm:266
>>>> STACK toplevel /GUS/gus_home/bin/ga:11
>>>>
>>>> --------------------------------------
>>>>
>>>> STACK TRACE:
>>>> at /usr/local/bioperl15/Bio/Root/Root.pm line 342
>>>> Bio::Root::Root::throw
>>>> ('Bio::SeqFeature::Tools::Unflattener=HASH(0xb5e124c)',
>>>> 'structure_type 2 is currently unknown') called at /usr/local/
>>>> bioperl15/Bio/SeqFeature/Tools/Unflattener.pm line 1419
>>>> Bio::SeqFeature::Tools::Unflattener::unflatten_seq
>>>> ('Bio::SeqFeature::Tools::Unflattener=HASH(0xb5e124c)', '-seq',
>>>> 'Bio::Seq::RichSeq=HASH(0xb820b14)', '-use_magic', 1) called at /
>>>> GUS/gus_home/lib/perl/GUS/Supported/Plugin/
>>>> InsertSequenceFeatures.pm line 353
>>>> GUS::Supported::Plugin::InsertSequenceFeatures::unflatten
>>>> ('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xa011adc)',
>>>> 'Bio::Seq::RichSeq=HASH(0xb820b14)') called at /GUS/gus_home/lib/
>>>> perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line 720
>>>>
>>>> GUS::Supported::Plugin::InsertSequenceFeatures::processFeatureTrees
>>>> ('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xa011adc)',
>>>> 'Bio::Seq::RichSeq=HASH(0xb820b14)', 140, 177) called at /GUS/
>>>> gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
>>>> line 330
>>>> GUS::Supported::Plugin::InsertSequenceFeatures::run
>>>> ('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xa011adc)',
>>>> 'HASH(0xb047e98)') called at /GUS/gus_home/lib/perl/GUS/PluginMgr/
>>>> GusApplication.pm line 549
>>>> eval {...} called at /GUS/gus_home/lib/perl/GUS/PluginMgr/
>>>> GusApplication.pm line 541
>>>> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport
>>>> ('GUS::PluginMgr::GusApplication=HASH(0x9ff0c20)',
>>>> 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at /GUS/
>>>> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 459
>>>> GUS::PluginMgr::GusApplication::doMajorMode_Run
>>>> ('GUS::PluginMgr::GusApplication=HASH(0x9ff0c20)',
>>>> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at /GUS/
>>>> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 357
>>>> GUS::PluginMgr::GusApplication::doMajorMode
>>>> ('GUS::PluginMgr::GusApplication=HASH(0x9ff0c20)',
>>>> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at /GUS/
>>>> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 266
>>>> GUS::PluginMgr::GusApplication::parseAndRun
>>>> ('GUS::PluginMgr::GusApplication=HASH(0x9ff0c20)', 'ARRAY
>>>> (0xa004738)') called at /GUS/gus_home/bin/ga line 11
>>>>
>>>>
>>>>
>>>
>>> --
>>> Dr. Aaron J. Mackey, Ph.D.
>>> Project Manager, ApiDB Bioinformatics Resource Center
>>> Penn Genomics Institute, University of Pennsylvania
>>> email: amackey at pcbi.upenn.edu
>>> office: 215-898-1205 (Biology, 212 Goddard Labs)
>>> 215-746-7018 (PCBI, 1428 Blockley Hall)
>>> fax: 215-746-6697 (Penn Genomics Institute)
>>> postal: Penn Genomics Institute
>>> Goddard Labs 212
>>> 415 S. University Avenue
>>> Philadelphia, PA 19104-6017
>>>
More information about the Bioperl-l
mailing list