[maker-devel] Maker crash for long chrm.

[Vipul Patel]

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>:

> 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
> STACK: Widget::snap::load_phat_hits programs/maker/maker/bin/../
> lib/Widget/snap.pm:974
> STACK: Widget::snap::parse programs/maker/maker/bin/../lib/Widget/
> 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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