[maker-devel] unknown error

[Carson Holt]

Sorry for the slow response, but this message was caught by my spam filter
so I never saw it till now.

Which version of MAKER are you using?  Have you tied the most recent
online version/

--Carson


On 7/30/13 3:13 PM, "Gaelen Burke" <grburke at uga.edu> wrote:

>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/MpiCh
>unk.
>pm:2159
>STACK: Process::MpiChunk::run
>/panfs/pstor.storage/rcclocal/zcluster/maker/2.10/bin/../lib/Process/MpiCh
>unk.
>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
>
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