[maker-devel] unknown error

[Gaelen Burke]

Hello,
I have an error that occurs in my MAKER run for 52 of several thousand scaffolds. The annotation of these scaffolds fails, even after 3 re-tries. I also pulled out the failed sequences and started a run from scratch, with the same result. Could anyone tell me what this error means and how I could possibly fix it?
Thanks,
Gaelen Burke

Here is the message that occurs:

Processing transcripts into genes

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Calling translate without a seq argument!
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/perl/5.14.1/lib/site_perl/5.14.1/Bio/Root/Root.pm:472
STACK: Bio::Tools::CodonTable::translate /usr/local/perl/5.14.1/lib/site_perl/5.14.1/Bio/Tools/CodonTable.pm
:411
STACK: PhatHit_utils::_adjust /panfs/pstor.storage/rcclocal/zcluster/maker/2.10/bin/../lib/PhatHit_utils.pm:
880
STACK: PhatHit_utils::adjust_start_stop /panfs/pstor.storage/rcclocal/zcluster/maker/2.10/bin/../lib/PhatHit
_utils.pm:776
STACK: maker::auto_annotator::load_transcript_struct /panfs/pstor.storage/rcclocal/zcluster/maker/2.10/bin/.
./lib/maker/auto_annotator.pm:1808
STACK: maker::auto_annotator::group_transcripts /panfs/pstor.storage/rcclocal/zcluster/maker/2.10/bin/../lib
/maker/auto_annotator.pm:2163
STACK: maker::auto_annotator::annotate_genes /panfs/pstor.storage/rcclocal/zcluster/maker/2.10/bin/../lib/ma
ker/auto_annotator.pm:877
STACK: Process::MpiChunk::_go /panfs/pstor.storage/rcclocal/zcluster/maker/2.10/bin/../lib/Process/MpiChunk.
pm:2159
STACK: Process::MpiChunk::run /panfs/pstor.storage/rcclocal/zcluster/maker/2.10/bin/../lib/Process/MpiChunk.
pm:257
STACK: Process::MpiTiers::run_all /panfs/pstor.storage/rcclocal/zcluster/maker/2.10/bin/../lib/Process/MpiTi
ers.pm:193
STACK: /usr/local/maker/latest/bin/maker:276
-----------------------------------------------------------

FATAL ERROR
ERROR: Failed while clustering transcripts into genes for annotations!!

ERROR: Chunk failed at level 20
!!
FAILED CONTIG:scaffold_0040