[maker-devel] MAKER failing during Augustus run

[Carson Holt]

First try using Augustu v3.3.3 or the live version from GitHub (https://github.com/Gaius-Augustus/Augustus <https://github.com/Gaius-Augustus/Augustus>). You can specify the other augustus version in maker_exe.ctl.  You can use ctl+z to pause the run right when MAKER reaches the specified augustus call.  Or after trying the newer agusuts version, you can upload everything from the run to https://github.com/Gaius-Augustus/Augustus <https://github.com/Gaius-Augustus/Augustus> and I can try to extract the files for you.

Or if you are adventurous you can run in the perl debugger.

#start debugger
perl -dS maker

#continue to augustus calls
DB<1> c Widget::augustus::run

#continue to augustus failure (right before dieing)
DB<2> c 282

At this point just copy the command as files still exist

—Carson


> On Oct 2, 2020, at 2:54 AM, Lior Glick <liorglic at mail.tau.ac.il> wrote:
> 
> 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!
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20201002/e9e5fc2e/attachment-0003.html>