[maker-devel] Error Message using Maker3 with EvidenceModeler
Martinson, John
Hi. I am trying to update some gene models with new RNA data in maker3, using EvidenceModeler, and I am encountering the error below. I have tried various adjustments to my inputs, focusing on changes to the maker_evm.ctl file, the models-to-be-updated gff file, and the new RNA input (trying it as both sequence and genome-aligned gff files). None of the many changes I’ve tried, other than just “turning off” EVidenceModeler entirely, has made a difference, so I thought I’d ask for some help. Any idea on what might be happening here?
Thanks,
John Martinson
USEPA
Maker Google group email johnm...@yahoo.com
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ERROR: No hit source {_HMM} in maker::auto_annotator
at /data/progs/maker3/maker/bin/../lib/maker/auto_annotator.pm line 2873.
maker::auto_annotator::group_transcripts('ARRAY(0xe7b1788)', 'ARRAY(0x70110a0)', 'FastaSeq=HASH(0x6304360)', 'scaf101', 0, 'evm_abinit', '/data/maker/fourScafsGffBasedEvm.maker.output/fourScafsGffBas...', 'HASH(0x44634a0)') called at /data/progs/maker3/maker/bin/../lib/maker/auto_annotator.pm line 1182
maker::auto_annotator::annotate_genes('HASH(0x20f88800)', 'ARRAY(0x70110a0)', 'FastaSeq=HASH(0x6304360)', 'scaf101', 0, '/data/maker/fourScafsGffBasedEvm.maker.output/fourScafsGffBas...', 'HASH(0x44634a0)') called at /data/progs/maker3/maker/bin/../lib/Process/MpiChunk.pm line 3894
Process::MpiChunk::__ANON__() called at /data/progs/maker3/maker/bin/../lib/Error.pm line 415
eval {...} called at /data/progs/maker3/maker/bin/../lib/Error.pm line 407
Error::subs::try('CODE(0x123909e0)', 'HASH(0x6185338)') called at /data/progs/maker3/maker/bin/../lib/Process/MpiChunk.pm line 4277
Process::MpiChunk::_go('Process::MpiChunk=HASH(0x7310030)', 'run', 'HASH(0x5193580)', 2, 4) called at /data/progs/maker3/maker/bin/../lib/Process/MpiChunk.pm line 340
Process::MpiChunk::run('Process::MpiChunk=HASH(0x7310030)', 0) called at /data/progs/maker3/maker/bin/../lib/Process/MpiChunk.pm line 356
Process::MpiChunk::run_all('Process::MpiChunk=HASH(0x7310030)', 0) called at /data/progs/maker3/maker/bin/../lib/Process/MpiTiers.pm line 287
Process::MpiTiers::run_all('Process::MpiTiers=HASH(0x11058b50)', 0) called at /data/progs/maker3/maker/bin/../lib/Process/MpiTiers.pm line 287
Process::MpiTiers::run_all('Process::MpiTiers=HASH(0x44a4dc0)', 0) called at /data/progs/maker3/maker/bin/maker line 680
--> rank=NA, hostname=d2626ujmartins4.aa.ad.epa.gov
ERROR: Failed while clustering transcripts into genes for annotations
ERROR: Chunk failed at level:2, tier_type:4
FAILED CONTIG:scaf101
ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:scaf101