[maker-devel] MAKER annotation and Trinity output

[Ambrose Andongabo (RRes-Roth)]

Dear all,

I am using the latest version of MAKER and I keep on getting this error message when I activate fgenesh gene predictor in the maker_opts.ctl file. It runs successfully when using SNAP, GeneMark and AUGUSTUS. If I do not provide my ESTs evidence in the form of Trinity output, the pipeline will run successfully using all the four gene predictors including fgenesh.   I wonder if someone encountered such a problem before

#--------- command -------------#
Widget::fgenesh:
/home/data/MAKER_2.30/maker/bin/../lib/Widget/fgenesh/fgenesh_wrap /home/data/mg_annotation/fgenesh/fgenesh /home/data/mg_annotation/fgenesh/Fusarium /tmp/maker_cAePfY/0/164_0.557-1163.Fusarium.auto_annotator.fgenesh.fasta -exon_table:/tmp/maker_cAePfY/0/164_0.557-1163.Fusarium.auto_annotator.xdef.fgenesh > /tmp/maker_cAePfY/0/164_0.557-1163.Fusarium.auto_annotator.fgenesh
#-------------------------------#
ERROR: FGENESH Failed
ERROR: FgenesH failed
--> rank=NA, hostname=vnc.rothamsted.ac.uk
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:contig_1

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:contig_1

examining contents of the fasta file and run log

I will be grateful for your contribution

Thanks

Ambrose


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