[maker-devel] August failing for one contig only during Maker run

[Carson Holt]

The failure is internal to Augustus. Try updating Augustus to 3.3. If it still fails after that let me know. We will have to isolate the command and files used, so you can send it as a test dataset to the Augustus devlopers.

—Carson

> On Apr 20, 2018, at 8:47 AM, Aditi Rambani <ar834 at cornell.edu> wrote:
> 
> Hello, 
> 
> Maker successfully annotated the genome but keeps failing for one contig with error message attached below. Can you please help me troubleshoot this ? There is no issue with augustus for rest of the contigs. 
> 
> Thank you
> 
> Aditi 
> 
> #--------- command -------------#
> Widget::augustus:
> ~/augustus-3.2/bin/augustus --species=Cxxx --strand=forward --UTR=off --hintsfile=/tmp/maker_dSn0ps/0/71_0.26253049-26257472.Cxxx.auto_annotator.xdef.augustus --extrinsicCfgFile=/data/home/srs57/programs/augustus-3.2/config/extrinsic/extrinsic.MPE.cfg /tmp/maker_dSn0ps/0/71_0.26253049-26257472.Cxxx.auto_annotator.augustus.fasta > /tmp/maker_dSn0ps/0/71_0.26253049-26257472.Cxxx.auto_annotator.augustus
> #-------------------------------#
> Sampling error in intron model. state=14 base=4422
> 
> ~/augustus-3.2/bin/augustus: ERROR
> Tried to sample from empty list.
> 
> Sampling error in intron model. state=14 base=4422
> ~/augustus-3.2/bin/augustus: ERROR
> Tried to sample from empty list.
> 
> ERROR: Augustus failed
> --> rank=NA, hostname=xxx
> ERROR: Failed while annotating transcripts
> ERROR: Chunk failed at level:1, tier_type:4
> FAILED CONTIG:Contigxxx
> 
> ERROR: Chunk failed at level:6, tier_type:0
> FAILED CONTIG:Contigxxx
> 
> examining contents of the fasta file and run log

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