search

jonathancrabtree / Circleator

Flexible circular visualization of genome-associated data with BioPerl and SVG.
Other
46 stars 8 forks source link

MSG: Failed validation of sequence '1'. Invalid characters were: #39

Open Karimi-81 opened 2 years ago

Karimi-81 commented 2 years ago

Hi There, I try to use Circleator to plot a circos for my genome assembly. The genome includes several large-size chromosomes. After running the following command, I got some errors: ./Circleator/bin/circleator --data=genome.gbff --config=genes-only.txt --pad=100 > pa-genes-only.svg

------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed validation of sequence '1'. Invalid characters were: STACK: Error::throw STACK: Bio::Root::Root::throw /cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/bioperl/1.7.7/lib/perl5/site_perl/5.30.2/Bio/Root/Root.pm:449 STACK: Bio::PrimarySeq::validate_seq /cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/bioperl/1.7.7/lib/perl5/site_perl/5.30.2/Bio/PrimarySeq.pm:338 STACK: Bio::PrimarySeq::_set_seq_by_ref /cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/bioperl/1.7.7/lib/perl5/site_perl/5.30.2/Bio/PrimarySeq.pm:287 STACK: Bio::PrimarySeq::seq /cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/bioperl/1.7.7/lib/perl5/site_perl/5.30.2/Bio/PrimarySeq.pm:272 STACK: Bio::PrimarySeq::new /cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/bioperl/1.7.7/lib/perl5/site_perl/5.30.2/Bio/PrimarySeq.pm:229 STACK: Bio::Seq::new /cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/bioperl/1.7.7/lib/perl5/site_perl/5.30.2/Bio/Seq.pm:499 STACK: Bio::Seq::RichSeq::new /cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/bioperl/1.7.7/lib/perl5/site_perl/5.30.2/Bio/Seq/RichSeq.pm:128 STACK: ./Circleator/bin/circleator:705

Do you have any idea to solve the problem. I would be appreciated if you could help me in this regard.