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tseemann / prokka

:zap: :aquarius: Rapid prokaryotic genome annotation
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Genetic code 15. Failed validation of sequence '1'. Invalid characters were: '''''''''''''''''''''''''' #682

Open ZarulHanifah opened 10 months ago

ZarulHanifah commented 10 months ago

Hello prokka developers,

I am experimenting with different genetic codes for prophage sequences. I tried genetic code 4 and 11, works fine. Maybe for genetic code 4, I saw warnings like:

--------------------- WARNING ---------------------
MSG: Seq [subEli4]: Not using a valid terminator codon!
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Seq [subEli4]: Not using a valid initiator codon!
---------------------------------------------------

However, with the same sequence, on genetic code 15, I obtained the same warnings, with extra EXCEPTION:

------------- EXCEPTION -------------
MSG: Failed validation of sequence '1'. Invalid characters were: ''''''''''''''''''''''''''
STACK Bio::PrimarySeq::validate_seq /home/ahbui/Zarul/Software/miniconda3/envs/bio1/lib/perl5/site_perl/Bio/PrimarySeq.pm:338
STACK Bio::PrimarySeq::_set_seq_by_ref /home/ahbui/Zarul/Software/miniconda3/envs/bio1/lib/perl5/site_perl/Bio/PrimarySeq.pm:287
STACK Bio::PrimarySeq::seq /home/ahbui/Zarul/Software/miniconda3/envs/bio1/lib/perl5/site_perl/Bio/PrimarySeq.pm:272
STACK Bio::Seq::seq /home/ahbui/Zarul/Software/miniconda3/envs/bio1/lib/perl5/site_perl/Bio/Seq.pm:572
STACK Bio::PrimarySeqI::translate /home/ahbui/Zarul/Software/miniconda3/envs/bio1/lib/perl5/site_perl/Bio/PrimarySeqI.pm:709
STACK toplevel /home/ahbui/Zarul/Software/miniconda3/envs/bio1/bin/prokka:1081
-------------------------------------

Thank you.