[ensembl-dev] Genebuild problem - Could not find start or end exon in transcript_id

[wenkai jiang]

for some jobs, i got error info:

-------------------- WARNING ----------------------
MSG: Failed to write gene no-id_wisebest 9227   11453   -1      bambus_4191
-------------------- EXCEPTION --------------------
MSG: Could not find start or end exon in transcript_id=7948
STACK
Bio::EnsEMBL::DBSQL::TranslationAdaptor::fetch_all_alternative_by_Transcript
/home/SCE/jiangwenkai/ensembl/ensembl/modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm:160
STACK Bio::EnsEMBL::Transcript::get_all_alternative_translations
/home/SCE/jiangwenkai/ensembl/ensembl/modules/Bio/EnsEMBL/Transcript.pm:644
STACK Bio::EnsEMBL::DBSQL::TranscriptAdaptor::store
/home/SCE/jiangwenkai/ensembl/ensembl/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm:798
STACK Bio::EnsEMBL::DBSQL::GeneAdaptor::store
/home/SCE/jiangwenkai/ensembl/ensembl/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm:1204
STACK (eval)
/home/SCE/jiangwenkai/ensembl/ensembl-analysis/modules/Bio/EnsEMBL/Analysis/RunnableDB/GeneBuilder.pm:101
STACK Bio::EnsEMBL::Analysis::RunnableDB::GeneBuilder::write_output
/home/SCE/jiangwenkai/ensembl/ensembl-analysis/modules/Bio/EnsEMBL/Analysis/RunnableDB/GeneBuilder.pm:100
STACK (eval)
/home/SCE/jiangwenkai/ensembl/ensembl-pipeline/modules/Bio/EnsEMBL/Pipeline/Job.pm:641
STACK Bio::EnsEMBL::Pipeline::Job::run_module
/home/SCE/jiangwenkai/ensembl/ensembl-pipeline/modules/Bio/EnsEMBL/Pipeline/Job.pm:639
STACK (eval)
/home/SCE/jiangwenkai/ensembl/ensembl-pipeline/modules/Bio/EnsEMBL/Pipeline/
runner.pl:219
STACK main::run_jobs_with_lsfcopy
/home/SCE/jiangwenkai/ensembl/ensembl-pipeline/modules/Bio/EnsEMBL/Pipeline/
runner.pl:218
STACK toplevel
/home/SCE/jiangwenkai/ensembl/ensembl-pipeline/modules/Bio/EnsEMBL/Pipeline/
runner.pl:128
---------------------------------------------------
FILE: Analysis/RunnableDB/GeneBuilder.pm LINE: 103
CALLED BY: EnsEMBL/Pipeline/Job.pm  LINE: 641
---------------------------------------------------
WRITING: Lost the will to live Error
Job 1 failed: [
-------------------- EXCEPTION --------------------
MSG: Problems for GeneBuilder writing output for
scaffold:june:bambus_4191:1:20466:1 [
-------------------- EXCEPTION --------------------
MSG: Failed to write some genes
STACK Bio::EnsEMBL::Analysis::RunnableDB::GeneBuilder::write_output
/home/SCE/jiangwenkai/ensembl/ensembl-analysis/modules/Bio/EnsEMBL/Analysis/RunnableDB/GeneBuilder.pm:110
STACK (eval)
/home/SCE/jiangwenkai/ensembl/ensembl-pipeline/modules/Bio/EnsEMBL/Pipeline/Job.pm:641
STACK Bio::EnsEMBL::Pipeline::Job::run_module
/home/SCE/jiangwenkai/ensembl/ensembl-pipeline/modules/Bio/EnsEMBL/Pipeline/Job.pm:639
STACK (eval)
/home/SCE/jiangwenkai/ensembl/ensembl-pipeline/modules/Bio/EnsEMBL/Pipeline/
runner.pl:219
STACK main::run_jobs_with_lsfcopy
/home/SCE/jiangwenkai/ensembl/ensembl-pipeline/modules/Bio/EnsEMBL/Pipeline/
runner.pl:218
STACK toplevel
/home/SCE/jiangwenkai/ensembl/ensembl-pipeline/modules/Bio/EnsEMBL/Pipeline/
runner.pl:128
---------------------------------------------------
]
STACK Bio::EnsEMBL::Pipeline::Job::run_module
/home/SCE/jiangwenkai/ensembl/ensembl-pipeline/modules/Bio/EnsEMBL/Pipeline/Job.pm:662
STACK (eval)
/home/SCE/jiangwenkai/ensembl/ensembl-pipeline/modules/Bio/EnsEMBL/Pipeline/
runner.pl:219
STACK main::run_jobs_with_lsfcopy
/home/SCE/jiangwenkai/ensembl/ensembl-pipeline/modules/Bio/EnsEMBL/Pipeline/
runner.pl:218
STACK toplevel
/home/SCE/jiangwenkai/ensembl/ensembl-pipeline/modules/Bio/EnsEMBL/Pipeline/
runner.pl:128
---------------------------------------------------
]Finished job 1
I use sequenced scaffold to build gene models, these scaffolds contained
several gaps.

These errors means what?
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