[maker-devel] Maker train SNAP: substr outside of string at Carp.pm

[Xabier Vázquez-Campos]

Hi Yuna,
adding to Carson's answer, check the output of maker2zff. If you don't have
RNAseq data or any other high-quality evidences for annotation, chances are
that the default parameters of maker2zff are too strict and are producing
empty output files.
Check the maker2zff --help and adjust the options as needed. In "worst case
scenario" you may need to run it with "-n", which has no filtering at all
in regards about which genes from the gff file to select.
Cheers,
Xabi

On Wed, 26 Jun 2019 at 07:17, Carson Holt <carsonhh at gmail.com> wrote:

> It dies trying to read SNAP’s result file. Check earlier in the log to see
> if there are any other errors. If not, run maker without MPI on a single
> CPU. You should be able to copy the command MAKER is using to call SNAP
> right before the failure. You can try running it outside of MAKER. My guess
> is there is a problem with SNAP failing and leaving a truncated report, or
> something in wrong with the training file SNAP is using.
>
> —Carson
>
>
> > On Jun 25, 2019, at 7:54 AM, Yuna <yuna.seagullbande at gmail.com> wrote:
> >
> > Hi,
> >
> > 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.
> >
> > I  appreciate any help. Thank you!
> >
> > Log:
> > 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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>
>
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-- 
Xabier Vázquez-Campos, *PhD*
*Research Associate*
NSW Systems Biology Initiative
School of Biotechnology and Biomolecular Sciences
The University of New South Wales
Sydney NSW 2052 AUSTRALIA
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