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

[Carson Holt]

Sorry for the slow reply.  I'm not on a long drive, but I am away this
week.  Could you send me the genemark hmm file and one of the contigs that
fails.

Thanks,
Carson


On 12-11-04 3:20 AM, "Gowthaman Ramasamy"
<gowthaman.ramasamy at seattlebiomed.org> wrote:

>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/gm
>hmm_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//th
>eVoid.Enmo_susu.05/Enmo_susu%2E05.all.Enmo-1%2E0%2E2_susu_GenemarkS_prokar
>yotic%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//th
>eVoid.Enmo_susu.05/query.fasta
>#-------------------------------#
>substr outside of string at
>/nethome/gramasamy/software/maker-2.10/maker/bin/../lib/CGL/TranslationMac
>hine.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