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

[Carson Holt]

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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