[maker-devel] MAKER v3 Fgenesh ERROR

[Carson Holt]

Sorry for the slow reply. This got lost somehow. The file from the mailing list is 5 years old. Don’t use it. You are actually downgrading, not upgrading. You will break things.

Run maker outside of MPI (if you are using MPI). There might be additional error message, that are further back that are getting covered by extra MPI output.  I don’t actually have a license for fgenesh to test with any more, so debugging it for you may be difficult.  My guess is that a more recent version has slightly different output format which is breaking the parser. Also you need to restore the previous fgenesh.pm file before you can run any tests (may need to reinstall MAKER).  

Also try MAKER3 vs MAKER2. They both run fgenesh slightly differently.

Basically after a couple of tests/error messages I may be able to send you something that would at least allow you to run fgenesh outside of MAKER to see what’s going on.

—Carson



> On Feb 7, 2019, at 12:43 PM, Kapeel Chougule <kapeelc at gmail.com> wrote:
> 
> Hi, Carson
> 
> I have been getting this error with fgenesh tool within MAKER. It runs ok with most of the assembly contigs but seems to fail on one contig or part of the contig with the below error
> 
> Widget::fgenesh:
> /mnt/grid/ware/hpc/home/data/mcampbel/applications/maker/bin/../lib/Widget/fgenesh/fgenesh_wrap /mnt/grid/ware/hpc_norepl/data/data/programs/fgenesh_v8/fgenesh_suite_v8.0.0a/fgenesh /sonas-hs/ware/hpc_norepl/data/programs/fgenesh_v8/fgenesh_suite_v8.0.0a/Zeamays.mpar.dat.new /tmp/uge/53139300.1.primary.q/maker_j3ttxX/6/6_1.600610-613023.Zeamays.mpar.dat.new.auto_annotator.fgenesh.fasta -exon_table:/tmp/uge/53139300.1.primary.q/maker_j3ttxX/6/6_1.600610-613023.Zeamays.mpar.dat.new.auto_annotator.xdef.fgenesh > /tmp/uge/53139300.1.primary.q/maker_j3ttxX/6/6_1.600610-613023.Zeamays.mpar.dat.new.auto_annotator.fgenesh
> #-------------------------------#
>  ...processing 9 of 24
>  ...processing 8 of 28
>  ...processing 10 of 24
>  ...processing 9 of 28
>  ...processing 11 of 24
>  ...processing 10 of 28
>  ...processing 12 of 24
>  ...processing 11 of 28
> deleted:0 genes
> ERROR: FgenesH failed
> --> rank=14, hostname=bnbcompute50
> ERROR: Failed while annotating transcripts
> ERROR: Chunk failed at level:1, tier_type:4
> FAILED CONTIG:Super-Scaffold_14.2_contig2
> 
> I updated the perl module fgenesh.pm <http://fgenesh.pm/> as suggested in the previous threads. Attached are the  maker_opts.ctl and STDERR log file.
> 
> Thanks
> 
> Kapeel
> 
>  
> 
> -- 
> 
> Kapeel Chougule
> Computational Scientist Developer II
> One Bungtown Road Cold Spring Harbor, NY 11724
> http://www.warelab.org/ <http://www.warelab.org/>
> 
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