[maker-devel] Maker crash for long chrm.

[Vipul Patel]

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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