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Gowthaman Ramasamy  
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 More options Nov 4 2012, 4:24 am
From: Gowthaman Ramasamy <gowthaman.ramas...@seattlebiomed.org>
Date: Sun, 4 Nov 2012 01:20:19 -0800
Local: Sun, Nov 4 2012 4:20 am
Subject: [maker-devel] Chunk failed at level 6 error..
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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/gmh mm_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_11/0 5/Enmo_susu.05.maker.output/Enmo_susu.05_datastore/8F/8F/Enmo_susu.05//theV oid.Enmo_susu.05/Enmo_susu%2E05.all.Enmo-1%2E0%2E2_susu_GenemarkS_prokaryot ic%2Emod_hmm%2Emod.genemark /autoxfs/bifx/NGS/WUSTL/Enmo/Annotation/05_GMprok/01_gene_pred_Prok_05_11/0 5/Enmo_susu.05.maker.output/Enmo_susu.05_datastore/8F/8F/Enmo_susu.05//theV oid.Enmo_susu.05/query.fasta
#-------------------------------#
substr outside of string at /nethome/gramasamy/software/maker-2.10/maker/bin/../lib/CGL/TranslationMach ine.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
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Gowthaman Ramasamy  
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 More options Nov 4 2012, 5:03 am
From: Gowthaman Ramasamy <gowthaman.ramas...@seattlebiomed.org>
Date: Sun, 4 Nov 2012 02:01:46 -0800
Local: Sun, Nov 4 2012 5:01 am
Subject: Re: [maker-devel] Chunk failed at level 6 error..
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Hi Carson,
when I tried running genemark as below, I see the *.lst files (protein  & nuc fasta) produced. But no gtf2 at all...
And no gms.log files at all.

Any ideas?

/nethome/gramasamy/software/genemark_suite_linux_64/gmsuite/gmhmmp -p 0 -m ./genemarkhmms/Enmo-1.0.2_susu_GenemarkS_prokaryotic.mod_hmm.mod -a  Enmo_susu.11.fsa

Thanks,
Gowthaman
________________________________________
From: maker-devel-boun...@yandell-lab.org [maker-devel-boun...@yandell-lab.org] On Behalf Of Gowthaman Ramasamy [gowthaman.ramas...@seattlebiomed.org]
Sent: Sunday, November 04, 2012 1:20 AM
To: maker-de...@yandell-lab.org
Subject: [maker-devel] Chunk failed at level 6 error..

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/gmh mm_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_11/0 5/Enmo_susu.05.maker.output/Enmo_susu.05_datastore/8F/8F/Enmo_susu.05//theV oid.Enmo_susu.05/Enmo_susu%2E05.all.Enmo-1%2E0%2E2_susu_GenemarkS_prokaryot ic%2Emod_hmm%2Emod.genemark /autoxfs/bifx/NGS/WUSTL/Enmo/Annotation/05_GMprok/01_gene_pred_Prok_05_11/0 5/Enmo_susu.05.maker.output/Enmo_susu.05_datastore/8F/8F/Enmo_susu.05//theV oid.Enmo_susu.05/query.fasta
#-------------------------------#
substr outside of string at /nethome/gramasamy/software/maker-2.10/maker/bin/../lib/CGL/TranslationMach ine.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
_______________________________________________
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maker-de...@box290.bluehost.com
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
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Carson Holt  
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 More options Nov 7 2012, 10:30 am
From: Carson Holt <carso...@gmail.com>
Date: Wed, 07 Nov 2012 10:29:34 -0500
Local: Wed, Nov 7 2012 10:29 am
Subject: Re: [maker-devel] Chunk failed at level 6 error..
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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"

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