Problems with refseq annotation when running Islandpath-DIMOB

Question

[hugo.avila]

Hi, I'm trying to run Islandpath-DIMOB (conda version=1.0.4) on refseq genomes and I get this error massage on some files (.gbff):

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: start [5340971] is greater than end [1335]. 
If you want to truncated and reverse complement, 
you must call trunc followed by revcom. Sorry.
STACK: Error::throw
STACK: Bio::Root::Root::throw /home/user/miniconda3/envs/IsL/lib/site_perl/5.26.2/Bio/Root/Root.pm:447
STACK: Bio::PrimarySeqI::trunc /home/user/miniconda3/envs/IsL/lib/site_perl/5.26.2/Bio/PrimarySeqI.pm:456
STACK: GenomeUtils::read_and_convert /home/user/miniconda3/envs/IsL/opt/islandpath/lib/GenomeUtils.pm:422
STACK: /home/user/miniconda3/envs/IsL/bin/islandpath:129
-----------------------------------------------------------

Apparently, the error is caused by the fact that some orfs have an start coordinate value greater than the end in the .gbff file. I work around the problem by re-annotating all genomes with Prokka, but the process is resource intensive with larger data sets. I need a way to directly repair .gbff files (start < end) or fix Islandpath-dimob to allow these refseq annotations.