[maker-devel] MAKER v3 Fgenesh ERROR

[Kapeel Chougule]

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/>*
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