[maker-devel] Maker crash for long chrm.

[Carson Holt]

I’m glad it’s working for you. Let us know if anything else comes up.

—Carson

> On Jan 20, 2017, at 6:34 AM, Vipul Patel <patel.kumar.vipul at gmail.com> wrote:
> 
> Solved. After some digging and printing I found out the problem.
> 
> It was snap itself!
> 
> For anybody who maybe runs in the  same problem, check snap. Apparently it was not correctly compiled and therefore it produced a not conform output! Recompiling solved my issue. 
> 
> Kind regards
> 
> 2017-01-20 9:44 GMT+01:00 Vipul Patel <patel.kumar.vipul at gmail.com <mailto:patel.kumar.vipul at gmail.com>>:
> Hi,
> 
> I hope someone can help me to figure out what is actually going wrong. 
> 
> I installed Maker 2.31.9, MPICH , BioPerl 1.7 via CPAN, pointed the TMP variable not to use NFS. The given testcase as well for 1k<small contigs < 1MB runs without any problems. 
> 
> Applying it to a sequence, for example with 57MB it failes, I tried it as well with a different sequences around 60MB, same outcome. 
> 
> I looked into the logs, but it was not really helpful as it was just stated that the job failed
> 
> It crashed with following message:
> 
> deleted:0 genes
> substr outside of string at /usr/share/perl/5.18/Carp.pm line 165.
> 
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Calling translate without a seq argument!
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /usr/local/share/perl/5.18.2/Bio/Root/Root.pm:447
> STACK: Bio::Tools::CodonTable::translate /usr/local/share/perl/5.18.2/Bio/Tools/CodonTable.pm:419
> STACK: CGL::TranslationMachine::longest_translation_plus_stop programs/maker/maker/bin/../lib/CGL/TranslationMachine.pm:280
> STACK: maker::auto_annotator::get_translation_seq programs/maker/maker/bin/../lib/maker/auto_annotator.pm:3236 <http://auto_annotator.pm:3236/>
> STACK: Widget::snap::load_phat_hits programs/maker/maker/bin/../lib/Widget/snap.pm:974 <http://snap.pm:974/>
> STACK: Widget::snap::parse programs/maker/maker/bin/../lib/Widget/snap.pm:690 <http://snap.pm:690/>
> STACK: GI::parse_abinit_file programs/maker/maker/bin/../lib/GI.pm:1194
> STACK: Process::MpiChunk::_go programs/maker/maker/bin/../lib/Process/MpiChunk.pm:1469
> STACK: Process::MpiChunk::run programs/maker/maker/bin/../lib/Process/MpiChunk.pm:341
> STACK: programs/maker/maker/bin/maker:979
> -----------------------------------------------------------
> --> rank=16, hostname=dummy
> ERROR: Failed while gathering ab-init output files
> ERROR: Chunk failed at level:1, tier_type:2
> FAILED CONTIG:chr_test
> 
> ERROR: Chunk failed at level:4, tier_type:0
> FAILED CONTIG:chr_test
> 
> examining contents of the fasta file and run log
> 
> 
> 
> --Next Contig--
> 
> Processing run.log file...
> 
> I got the same message if I run it without MPI, So I can guess it is not an MPI issue. 
> How can I find out if some jobs died so maybe this could lead to this problem?
> Other ideas how I can tackle this problem?
> 
> Kind regards
> 
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