------------ EXCEPTION: Bio::Root::Exception ------------- MSG: Failed validation of sequence '1'. Invalid characters were: ''' - Githubissues

NBISweden / AGAT

Another Gtf/Gff Analysis Toolkit

GNU General Public License v3.0

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------------ EXCEPTION: Bio::Root::Exception ------------- MSG: Failed validation of sequence '1'. Invalid characters were: ''' #395

Closed Psedhai closed 1 year ago

Psedhai commented 1 year ago

- how to solve this issue?

Thank you in advance

------------ EXCEPTION: Bio::Root::Exception ------------- MSG: Failed validation of sequence '1'. Invalid characters were: '''''''''' STACK: Error::throw STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:449 STACK: Bio::PrimarySeq::validate_seq /usr/share/perl5/Bio/PrimarySeq.pm:338 STACK: Bio::PrimarySeq::_set_seq_by_ref /usr/share/perl5/Bio/PrimarySeq.pm:287 STACK: Bio::PrimarySeq::seq /usr/share/perl5/Bio/PrimarySeq.pm:272 STACK: Bio::Seq::seq /usr/share/perl5/Bio/Seq.pm:572 STACK: Bio::PrimarySeqI::translate /usr/share/perl5/Bio/PrimarySeqI.pm:709 STACK: Bio::Roary::ExtractProteomeFromGFF::_fastatranslate /usr/share/perl5/Bio/Roary/ExtractProteomeFromGFF.pm:156 STACK: Bio::Roary::ExtractProteomeFromGFF::_convert_nucleotide_to_protein /usr/share/perl5/Bio/Roary/ExtractProteomeFromGFF.pm:164 STACK: Bio::Roary::ExtractProteomeFromGFF::fasta_file /usr/share/perl5/Bio/Roary/ExtractProteomeFromGFF.pm:29 STACK: Bio::Roary::CommandLine::ExtractProteomeFromGff::run /usr/share/perl5/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm:90 STACK: /usr/bin/extract_proteome_from_gff:14

Combine proteins into a single file

Juke34 commented 1 year ago

Sorry I don't get the point with AGAT? Your issue seems to be related to Roary. (By the way the error come from bioperl while in use by Roary) The message seem clear, you have invalid character in your sequence (or maybe you do not have any sequence at all)