[maker-devel] MAKER annotation and Trinity output

[Carson Holt]

Hi Ambrose,

It is likely caused by an issue with hints being generated for Fgenesh, I’ve
attached an updated module to be placed here —>
.../maker/lib/Widget/fgenesh.pm.

I will also integrate this into the MAKER download.

Thanks,
Carson

From:  "Ambrose Andongabo (RRes-Roth)" <Ambrose.Andongabo at rothamsted.ac.uk>
Date:  Thursday, January 23, 2014 at 4:19 AM
To:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  [maker-devel] MAKER annotation and Trinity output

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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