substr outside of string at Carp.pm

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substr outside of string at Carp.pm

Bianca Frommer
Dear support team,

I ran MAKER successfully to generate data for training SNAP. However,
now I want to run the training round with MAKER (run MAKER with the hmm
file), but MAKER fails for every contig it processed till now. The
"evidence_3.gff.ann" and "evidence_3.gff.def" files are empty (except
the gff header line) and the error massage is attached below. I can not
figure out what the problem is.

Thank you!
Sincerely,
Bianca

gathering ab-init output files

deleted:0 genes
substr outside of string at /usr/share/perl5/vendor_perl/Carp.pm line 346.

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Calling translate without a seq argument!
STACK: Error::throw
STACK: Bio::Root::Root::throw
/vol/perl/v5.28.1/lib/perl5/Bio/Root/Root.pm:447
STACK: Bio::Tools::CodonTable::translate
/vol/perl/v5.28.1/lib/perl5/Bio/Tools/CodonTable.pm:419
STACK: CGL::TranslationMachine::longest_translation_plus_stop
/vol/biotools/lib/maker-2.31.10/bin/../lib/CGL/TranslationMachine.pm:280
STACK: maker::auto_annotator::get_translation_seq
/vol/biotools/lib/maker-2.31.10/bin/../lib/maker/auto_annotator.pm:3236
STACK: Widget::snap::load_phat_hits
/vol/biotools/lib/maker-2.31.10/bin/../lib/Widget/snap.pm:974
STACK: Widget::snap::parse
/vol/biotools/lib/maker-2.31.10/bin/../lib/Widget/snap.pm:690
STACK: GI::parse_abinit_file
/vol/biotools/lib/maker-2.31.10/bin/../lib/GI.pm:1194
STACK: Process::MpiChunk::_go
/vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:1469
STACK: Process::MpiChunk::run
/vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:341
STACK: Process::MpiChunk::run_all
/vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:357
STACK: Process::MpiTiers::run_all
/vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiTiers.pm:287
STACK: Process::MpiTiers::run_all
/vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiTiers.pm:287
STACK: /vol/biotools/lib/maker-2.31.10/bin/maker:686
-----------------------------------------------------------
--> rank=NA, hostname=snorf
ERROR: Failed while gathering ab-init output files
ERROR: Chunk failed at level:1, tier_type:2
FAILED CONTIG:chr1

ERROR: Chunk failed at level:4, tier_type:0
FAILED CONTIG:chr1

examining contents of the fasta file and run log



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