[maker-devel] failed contigs

[Michael Thon]

running maker 2.26 some contigs seem to consistently fail to run, according to XXX_master_datastore_index.log

Here are the last few lines of run.log for one of the failed contigs:

CTL_OPTIONS     run     
LOGCHILD        /home/mike/projects/cg_maker/cgram.maker.output/cgram_datastore/supercont1.6/theVoid.supercont1.6/run.log.child.0       
LOGCHILD        /home/mike/projects/cg_maker/cgram.maker.output/cgram_datastore/supercont1.6/theVoid.supercont1.6/run.log.child.0       
LOGCHILD        /home/mike/projects/cg_maker/cgram.maker.output/cgram_datastore/supercont1.6/theVoid.supercont1.6/run.log.child.0       
LOGCHILD        /home/mike/projects/cg_maker/cgram.maker.output/cgram_datastore/supercont1.6/theVoid.supercont1.6/run.log.child.1       
LOGCHILD        /home/mike/projects/cg_maker/cgram.maker.output/cgram_datastore/supercont1.6/theVoid.supercont1.6/run.log.child.1       
LOGCHILD        /home/mike/projects/cg_maker/cgram.maker.output/cgram_datastore/supercont1.6/theVoid.supercont1.6/run.log.child.1       
DIED    RANK    0
DIED    COUNT   1


the contents of run.log.child.1 for the same contig:
STARTED cgram.maker.output/cgram_datastore/supercont1.6/theVoid.supercont1.6/supercont1%2E6.1.Repeat_Type_Elements%2Efasta.specific.out 
FINISHED        cgram.maker.output/cgram_datastore/supercont1.6/theVoid.supercont1.6/supercont1%2E6.1.Repeat_Type_Elements%2Efasta.specific.out 
STARTED cgram.maker.output/cgram_datastore/supercont1.6/theVoid.supercont1.6/supercont1%2E6.1.te_proteins%2Efasta.repeatrunner  
DIED    RANK    0:2:0:1
DIED    COUNT   1

So perhaps its a problem with the repeat masking step.  I already have annotated repeats using RepeatMasker and I have the gff2 file produced by RepeatMasker.  Do I need to convert this to gff3 before adding to to my maker_opts file?  Better yet, does anyone know why these contigs are failing and how to fix it?
Mike