[maker-devel] Chunk failed at level 6 error..

[Gowthaman Ramasamy]

Hi Carson,
As it happens, I am sorry to bother you again on a weekend. Here is my hoping that you are not on a long drive this time.

I am running genemark prokaryote via maker on a genome with 36 chromosomes. All but two finishes well.

On those two, i am not able to find anything unusual. Following is the error message i see. Could you please point to me what could be the possible source of these errors. Thanks verymuch in advance...

Widget::genemark:
/depot/perl-5.12.1/bin/perl /nethome/gramasamy/software/maker-2.10/maker/bin/../lib/Widget/genemark/gmhmm_wrap -m ./genemarkhmms/Enmo-1.0.2_susu_GenemarkS_prokaryotic.mod_hmm.mod -g /nethome/gramasamy/software/genemark_suite_linux_64/gmsuite/gmhmmp -p /nethome/gramasamy/software/genemark_suite_linux_64/gmsuite/probuild -o /autoxfs/bifx/NGS/WUSTL/Enmo/Annotation/05_GMprok/01_gene_pred_Prok_05_11/05/Enmo_susu.05.maker.output/Enmo_susu.05_datastore/8F/8F/Enmo_susu.05//theVoid.Enmo_susu.05/Enmo_susu%2E05.all.Enmo-1%2E0%2E2_susu_GenemarkS_prokaryotic%2Emod_hmm%2Emod.genemark /autoxfs/bifx/NGS/WUSTL/Enmo/Annotation/05_GMprok/01_gene_pred_Prok_05_11/05/Enmo_susu.05.maker.output/Enmo_susu.05_datastore/8F/8F/Enmo_susu.05//theVoid.Enmo_susu.05/query.fasta
#-------------------------------#
substr outside of string at /nethome/gramasamy/software/maker-2.10/maker/bin/../lib/CGL/TranslationMachine.pm line 223.

FATAL ERROR
ERROR: Failed while preparing masked sequence and ab-inits!!

ERROR: Chunk failed at level 6
!!
FAILED CONTIG:Enmo_susu.05


Thanks once again,
Gowthaman