Hello,
I encountered a problem while running VEP annotation on the entire human genome. The annotation runs smoothly for 21 chromosomes, but only fails on chromosome 16 with the following warning:
Plugin 'LoF' went wrong: MSG: Slice start cannot be greater than slice end
This seems to be caused by an issue in coordinate handling, possibly during the splice site evaluation in the plugin. I noticed that similar issues were mentioned in #102 and #31 ， but no clear resolution was provided.
Could someone help clarify this issue or suggest a workaround?
I’ve included my command and relevant run information below for reference:
WARNING: 83460 : WARNING: Plugin 'LoF' went wrong:
-------------------- EXCEPTION --------------------
MSG: Slice start cannot be greater than slice end
STACK Bio::EnsEMBL::Slice::expand /opt/vep/src/ensembl-vep/Bio/EnsEMBL/Slice.pm:1217
STACK LoF::get_upstream_acceptor_flank /plugins/extended_splice.pl:209
STACK LoF::get_effect_on_splice /plugins/extended_splice.pl:111
STACK LoF::run /plugins/LoF.pm:188
STACK (eval) /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/OutputFactory.pm:2138
STACK Bio::EnsEMBL::VEP::OutputFactory::run_plugins /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/OutputFactory.pm:2137
STACK Bio::EnsEMBL::VEP::OutputFactory::get_all_VariationFeatureOverlapAllele_output_hashes /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/OutputFactory.pm:396
STACK Bio::EnsEMBL::VEP::OutputFactory::get_all_output_hashes_by_VariationFeature /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/OutputFactory.pm:347
STACK Bio::EnsEMBL::VEP::OutputFactory::get_all_output_hashes_by_InputBuffer /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/OutputFactory.pm:299
STACK Bio::EnsEMBL::VEP::OutputFactory::get_all_lines_by_InputBuffer /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/OutputFactory.pm:269
STACK Bio::EnsEMBL::VEP::Runner::_buffer_to_output /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:422
STACK (eval) /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:671
STACK Bio::EnsEMBL::VEP::Runner::_forked_process /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:665
STACK Bio::EnsEMBL::VEP::Runner::_forked_buffer_to_output /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:496
STACK Bio::EnsEMBL::VEP::Runner::next_output_line /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:367
STACK Bio::EnsEMBL::VEP::Runner::run /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:208
STACK toplevel /opt/vep/src/ensembl-vep/vep:46
Date (localtime) = Fri Jun 27 15:28:22 2025
Ensembl API version = 114
Hello,
I encountered a problem while running VEP annotation on the entire human genome. The annotation runs smoothly for 21 chromosomes, but only fails on chromosome 16 with the following warning:
Plugin 'LoF' went wrong: MSG: Slice start cannot be greater than slice end
This seems to be caused by an issue in coordinate handling, possibly during the splice site evaluation in the plugin. I noticed that similar issues were mentioned in #102 and #31 ， but no clear resolution was provided.
Could someone help clarify this issue or suggest a workaround?
I’ve included my command and relevant run information below for reference:
WARNING: 83460 : WARNING: Plugin 'LoF' went wrong:
-------------------- EXCEPTION --------------------
MSG: Slice start cannot be greater than slice end
STACK Bio::EnsEMBL::Slice::expand /opt/vep/src/ensembl-vep/Bio/EnsEMBL/Slice.pm:1217
STACK LoF::get_upstream_acceptor_flank /plugins/extended_splice.pl:209
STACK LoF::get_effect_on_splice /plugins/extended_splice.pl:111
STACK LoF::run /plugins/LoF.pm:188
STACK (eval) /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/OutputFactory.pm:2138
STACK Bio::EnsEMBL::VEP::OutputFactory::run_plugins /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/OutputFactory.pm:2137
STACK Bio::EnsEMBL::VEP::OutputFactory::get_all_VariationFeatureOverlapAllele_output_hashes /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/OutputFactory.pm:396
STACK Bio::EnsEMBL::VEP::OutputFactory::get_all_output_hashes_by_VariationFeature /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/OutputFactory.pm:347
STACK Bio::EnsEMBL::VEP::OutputFactory::get_all_output_hashes_by_InputBuffer /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/OutputFactory.pm:299
STACK Bio::EnsEMBL::VEP::OutputFactory::get_all_lines_by_InputBuffer /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/OutputFactory.pm:269
STACK Bio::EnsEMBL::VEP::Runner::_buffer_to_output /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:422
STACK (eval) /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:671
STACK Bio::EnsEMBL::VEP::Runner::_forked_process /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:665
STACK Bio::EnsEMBL::VEP::Runner::_forked_buffer_to_output /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:496
STACK Bio::EnsEMBL::VEP::Runner::next_output_line /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:367
STACK Bio::EnsEMBL::VEP::Runner::run /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:208
STACK toplevel /opt/vep/src/ensembl-vep/vep:46
Date (localtime) = Fri Jun 27 15:28:22 2025
Ensembl API version = 114