[maker-devel] ERROR: Failed while clustering transcripts into genes for annotations

[John Martin]

I'm working on annotation for a de novo genomic assembly, and I have my 
jobs split into roughly equal (by seq length) batches.   I am seeing 
~2/3rds of these batches completing successfully, while the other 1/3rd 
is failing.   I identified a problem contig, and have been doing test 
maker runs on that to try and figure out whats going on.

The full batch was run using an older version of maker (v2.26), so I 
first tried updating to the latest version of maker (v2.31.8).  That 
version did point out one problem in an EST evidence file I was using, 
which I fixed.  That allowed maker to get much farther, but as it was 
nearing the end of the run it crashed again with this error message:

++++++++++++++++++++++++++++++++++
setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
  ...processing 0 of 8
  ...processing 1 of 8
  ...processing 2 of 8
  ...processing 3 of 8
  ...processing 4 of 8
  ...processing 5 of 8
  ...processing 6 of 8
  ...processing 7 of 8
  ...processing 0 of 13
  ...processing 1 of 13
  ...processing 2 of 13
  ...processing 3 of 13
  ...processing 4 of 13
  ...processing 5 of 13
  ...processing 6 of 13
  ...processing 7 of 13
  ...processing 8 of 13
  ...processing 9 of 13
  ...processing 10 of 13
  ...processing 11 of 13
  ...processing 12 of 13
annotating transcripts
Making transcripts
clustering transcripts into genes for annotations
Processing transcripts into genes

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Calling translate without a seq argument!
STACK: Error::throw
STACK: Bio::Root::Root::throw 
/home/ec2-user/bin/BioPerl-1.6.923/Bio/Root/Root.pm:486
STACK: Bio::Tools::CodonTable::translate 
/home/ec2-user/bin/BioPerl-1.6.923/Bio/Tools/CodonTable.pm:414
STACK: PhatHit_utils::_adjust 
/home/ec2-user/bin/maker/bin/../lib/PhatHit_utils.pm:846
STACK: PhatHit_utils::adjust_start_stop 
/home/ec2-user/bin/maker/bin/../lib/PhatHit_utils.pm:794
STACK: maker::auto_annotator::load_transcript_struct 
/home/ec2-user/bin/maker/bin/../lib/maker/auto_annotator.pm:2198
STACK: maker::auto_annotator::group_transcripts 
/home/ec2-user/bin/maker/bin/../lib/maker/auto_annotator.pm:2676
STACK: maker::auto_annotator::annotate_genes 
/home/ec2-user/bin/maker/bin/../lib/maker/auto_annotator.pm:1018
STACK: Process::MpiChunk::_go 
/home/ec2-user/bin/maker/bin/../lib/Process/MpiChunk.pm:3847
STACK: Process::MpiChunk::run 
/home/ec2-user/bin/maker/bin/../lib/Process/MpiChunk.pm:341
STACK: Process::MpiChunk::run_all 
/home/ec2-user/bin/maker/bin/../lib/Process/MpiChunk.pm:357
STACK: Process::MpiTiers::run_all 
/home/ec2-user/bin/maker/bin/../lib/Process/MpiTiers.pm:287
STACK: Process::MpiTiers::run_all 
/home/ec2-user/bin/maker/bin/../lib/Process/MpiTiers.pm:287
STACK: /home/ec2-user/bin/maker/bin/maker:686
-----------------------------------------------------------
--> rank=NA, hostname=ip-172-31-35-77.us-west-2.compute.internal
ERROR: Failed while clustering transcripts into genes for annotations
ERROR: Chunk failed at level:2, tier_type:4
FAILED CONTIG:ANCCEYDFT_Contig1675

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:ANCCEYDFT_Contig1675

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...


Maker is now finished!!!



Start_time: 1445912338
End_time:   1445913817
Elapsed:    1479
++++++++++++++++++++++++++++++++++



The root of the error seems clearly stated:

MSG: Calling translate without a seq argument!

but I don't know what that means in real terms.  All my inputs appear 
valid.  The contig I am testing with has 1 plus strand gene represented 
in the evidence files.  And I've set a local TMP directory since I've 
read that sometimes these kinds of problems can stem from the program 
running out of TMP space.  I am pretty sure that is not happening here 
(I put TMP on a disk with 1.1Tb of space, and the test contig is only 
13kbp).

Can anyone help me figure out what is going on?


Thanks,
John Martin




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