[maker-devel] MAKER v3 Fgenesh ERROR

[Kapeel Chougule]

Thanks Carson,

I will try the settings you suggested.

Also, for those failed contigs I ran fgenesh standalone and passed the
results to pred_gff in maker_opts.ctl. The run was successful. The only
issue with this was the name attribute in column predicted by MAKER had a
very different ID compared to other genes predicted.

E.g
Chr10   maker   mRNA    33029   45468   .       -       .
ID=maker-Chr10-pred_gff_Fgenesh-gene-0.5-mRNA-1;Parent=maker-Chr10-pred_gff_Fgenesh-gene-0.5;
Name=Chr10mRNA_1;_AED=0.21;_eAED=0.21;_QI=76|0.88|1|1|1|1|10|315|418

Correct Name attribute :
Chr10   maker   mRNA    33029   45468   .       -       .
ID=maker-Chr10-pred_gff_Fgenesh-gene-0.5-mRNA-1;Parent=maker-Chr10-pred_gff_Fgenesh-gene-0.5;
Name=maker-Chr10-pred_gff_Fgenesh-gene-0.5-mRNA-1
;_AED=0.21;_eAED=0.21;_QI=76|0.88|1|1|1|1|10|315|418

This was also reflected in the fasta headers.

Best

Kapeel



On Mon, Mar 11, 2019 at 12:55 PM Carson Holt <carsonhh at gmail.com> wrote:

> 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 as suggested in the previous
> threads. Attached are the  maker_opts.ctl and STDERR log file.
>
> Thanks
>
> Kapeel
>
>
>
> --
>
>
>
> *Kapeel ChouguleComputational Scientist Developer II*
>
>
> *One Bungtown Road Cold Spring Harbor, NY 11724http://www.warelab.org/
> <http://www.warelab.org/>*
> <maker_opts.ctl><stderr.log>
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>
>
>

-- 



*Kapeel ChouguleComputational Scientist Developer II*


*One Bungtown Road Cold Spring Harbor, NY 11724http://www.warelab.org/
<http://www.warelab.org/>*
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