MAKER failing during Augustus run

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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 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 from the Augustus forum, but it doesn't seem to provide much help.
Would appreciate any ideas/workarounds.
Thanks!


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Re: MAKER failing during Augustus run

Carson Holt-2
First try using Augustu v3.3.3 or the live version from GitHub (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 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 <[hidden email]> 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 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 from the Augustus forum, but it doesn't seem to provide much help.
Would appreciate any ideas/workarounds.
Thanks!

_______________________________________________
maker-devel mailing list
[hidden email]
http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org


_______________________________________________
maker-devel mailing list
[hidden email]
http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org