[maker-devel] MAKER failing during Augustus run

[Lior Glick]

Hello,
I am using MAKER2 with Augustus 3.2.2. I keep getting an error message when
annotating a specific contig. The relevant section of the MAKER stderr
looks like this:

Widget::augustus:
/powerapps/share/centos7/miniconda/miniconda2-4.5.4-MakerMPI/bin/augustus
--species=arabidopsis --strand=backward --UTR=off
--hintsfile=/home/tmp_liorglic/maker_zfUstg/0/265_0.10292360-10294752.arabidopsis.auto_annotator.xdef.augustus
--extrinsicCfgFile=/powerapps/share/centos7/miniconda/miniconda2-4.5.4-MakerMPI/config/extrinsic/extrinsic.MPE.cfg
/home/tmp_liorglic/maker_zfUstg/0/265_0.10292360-10294752.arabidopsis.auto_annotator.augustus.fasta
>
/home/tmp_liorglic/maker_zfUstg/0/265_0.10292360-10294752.arabidopsis.auto_annotator.augustus
#-------------------------------#
Sampling error in intron model. state=37 base=2391

/powerapps/share/centos7/miniconda/miniconda2-4.5.4-MakerMPI/bin/augustus:
ERROR
        Tried to sample from empty list.

Sampling error in intron model. state=37 base=2391

/powerapps/share/centos7/miniconda/miniconda2-4.5.4-MakerMPI/bin/augustus:
ERROR
        Tried to sample from empty list.

ERROR: Augustus failed
--> rank=NA, hostname=compute-0-301.power5
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:chunk08

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:chunk08

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file
chunk.maker.output/chunk_datastore/76/17/chunk08//theVoid.chunk08/265_0.10292360-10294752.arabidopsis.auto_annotator.augustus
did not finish on the last run and must be erased


Maker is now finished!!!

I found this thread
<https://groups.google.com/g/maker-devel/c/WBD_GEvELDE> with
a similar error but slightly different augustus command. The suggestion
there was to isolate the augustus command. This sounds like good advice,
but most of the inputs to the command are stored in a temporary location
and are deleted at the end of the MAKER run. Is there any way to restore
them?
Alternatively, are there any known solutions/explanations to this error?
All I could find was this thread
<https://bioinf.uni-greifswald.de/bioinf/forum/viewtopic.php?f=4&t=150> from
the Augustus forum, but it doesn't seem to provide much help.
Would appreciate any ideas/workarounds.
Thanks!
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