MSG: Slice start cannot be greater than slice end
Opened this issue · 0 comments
Hi,
I am using loftee ((GRCh37;Ensembl API 108),and I am getting a warning for some variants related to slicing, which disables the plugin from working. Could this be related to strange input variants, or is this a potential bug?
WARNING: Plugin 'LoF' went wrong:
-------------------- EXCEPTION --------------------
MSG: Slice start cannot be greater than slice end
STACK Bio::EnsEMBL::Slice::expand /public/home/xx2019/software/ensembl-vep/Bio/EnsEMBL/Slice.pm:1217
STACK LoF::get_upstream_acceptor_flank /public/home/xx2019/software/ensembl-vep/Plugins/loftee/extended_splice.pl:209
STACK LoF::get_effect_on_splice /public/home/xx2019/software/ensembl-vep/Plugins/loftee/extended_splice.pl:111
STACK LoF::run /public/home/xx2019/software/ensembl-vep/Plugins/loftee/LoF.pm:188
STACK (eval) /public/home/xx2019/software/ensembl-vep/modules/Bio/EnsEMBL/VEP/OutputFactory.pm:2072
STACK Bio::EnsEMBL::VEP::OutputFactory::run_plugins /public/home/xx2019/software/ensembl-vep/modules/Bio/EnsEMBL/VEP/OutputFactory.pm
STACK Bio::EnsEMBL::VEP::OutputFactory::get_all_VariationFeatureOverlapAllele_output_hashes /public/home/xx2019/software/ensembl-vep/
STACK Bio::EnsEMBL::VEP::OutputFactory::get_all_output_hashes_by_VariationFeature /public/home/xx2019/software/ensembl-vep/modules/Bi
STACK Bio::EnsEMBL::VEP::OutputFactory::get_all_output_hashes_by_InputBuffer /public/home/xx2019/software/ensembl-vep/modules/Bio/Ens
STACK Bio::EnsEMBL::VEP::OutputFactory::get_all_lines_by_InputBuffer /public/home/xx2019/software/ensembl-vep/modules/Bio/EnsEMBL/VEP
STACK Bio::EnsEMBL::VEP::Runner::_buffer_to_output /public/home/xx2019/software/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:421
STACK Bio::EnsEMBL::VEP::Runner::next_output_line /public/home/xx2019/software/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:369
STACK Bio::EnsEMBL::VEP::Runner::run /public/home/xx2019/software/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:207
STACK toplevel /public/home/xx2019/software/ensembl-vep/vep:240
Date (localtime) = Sat Aug 19 05:29:12 2023
Ensembl API version = 108
I have seen this issue in a previous post#31, but was unresolved.
Is there any assistance on this please?
Thanks in advance,
Jenny