[maker-devel] maker error with fully masked sequence

[Anne Campagna]

Dear Maker Developers,

I am running Maker v2.31, with proteomes, rnaseq, repeat library and fgenesh.
I came across the following error (please note I change the path names due to confidentiality)
running fgenesh.
#--------- command -------------#
Widget::fgenesh:
/maker_path1/maker/2.31.10/bin/../fgenesh_path/fgenesh/8.0.0a/fgenesh /tools/bioinfo/app/fgenesh-2.6/fgenesh_model_file /maker_output_path/run_02/tmp/maker_l129tl/0/14_0.42724263-42725212.Dicots.auto_annotator.fgenesh.fasta -exon_table:/ maker_output_path/run_02/tmp/maker_l129tl/0/14_0.42724263-42725212.Dicots.auto_annotator.xdef.fgenesh > / maker_output_path /run_02/tmp/maker_l129tl/0/14_0.42724263-42725212.Dicots.auto_annotator.fgenesh
#-------------------------------#
ERROR: FgenesH failed
--> rank=NA, hostname=by0q4y.eu.seeds.basf.net
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:chrC03
ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:chrC03

I then looked at the fasta file for this particular chunk (see below) and the error seems to be due to that chunk being fully masked. What would be the workaround for this so that maker can handle this and doesn't fail the whole contig/chromosome?

$more 14_0.42724263-42725212.Dicots.auto_annotator.fgenesh.fasta
>chrC03 14_0 offset:42724263
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Thanks a lot for your help!
Anne



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