genemark warning: gmhmme warning: index 41 is out of range for max 40 for key BP_ACC_DISTR

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genemark warning: gmhmme warning: index 41 is out of range for max 40 for key BP_ACC_DISTR

Collett, James R-2
Thanks, everyone, for the help so far with MAKER. Having made it through SNAP, I'm now trying Genemark for the first time.

I just created a model trained on my genome by running gm_es.pl --min_contig 10000 --BP ON ../CBS_large_contigs_454_solexa.fasta . My draft assembly has 1092 contigs,  so I reduced the --min_contig to 10000 as the README recommended for assemblies with lots of small contigs, and turned on the --BP option as recommended for fungal genomes in Current Protocols in Bioinformatics 4.6.1-4.6.10, September 2011.  The gm_es.pl script ran to completion and created a genemark_hmm.gtf file, but it also generated this warning 2997 times:

gmhmme warning: index 41 is out of range for max 40 for key BP_ACC_DISTR

Can someone tell me what this warning means, and if I should be concerned about it?  I'm using gm_es_bp_linux64_v2.3d.

Thanks,

Jim


__________________________________________________
James R. Collett, Ph.D.
Senior Scientist
Chemical and Biological Process Development Group
Energy and Environment Directorate
Pacific Northwest National Laboratory
902 Battelle Boulevard
P.O. Box 999, MSIN P8-60
Richland, WA  99352 USA








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Re: genemark warning: gmhmme warning: index 41 is out of range for max 40 for key BP_ACC_DISTR

Sujai Kumar
I had the same problem. gm_es_bp_linux64_v2.3e (one version newer)
finished and gave a .gtf file (as well as the es.mod file used by
Maker) but had this error a few thousand times.

On running this model in Maker, I see sensible genemark predictions
(that line up with the Augustus / SNAP models in most cases) - so I've
decided not to worry about the errors.

If someone knows more about Genemark - could you let this group know?
(Genemark doesn't seem to have it's own group).

Cheers,

- Sujai

On Jan 28, 8:28 pm, "Collett, James R" <[hidden email]> wrote:

> Thanks, everyone, for the help so far with MAKER. Having made it through SNAP, I'm now trying Genemark for the first time.
>
> I just created a model trained on my genome by running gm_es.pl --min_contig 10000 --BP ON ../CBS_large_contigs_454_solexa.fasta . My draft assembly has 1092 contigs,  so I reduced the --min_contig to 10000 as the README recommended for assemblies with lots of small contigs, and turned on the --BP option as recommended for fungal genomes in Current Protocols in Bioinformatics 4.6.1-4.6.10, September 2011.  The gm_es.pl script ran to completion and created a genemark_hmm.gtf file, but it also generated this warning 2997 times:
>
> gmhmme warning: index 41 is out of range for max 40 for key BP_ACC_DISTR
>
> Can someone tell me what this warning means, and if I should be concerned about it?  I'm using gm_es_bp_linux64_v2.3d.
>
> Thanks,
>
> Jim
>
> __________________________________________________
> James R. Collett, Ph.D.
> Senior Scientist
> Chemical and Biological Process Development Group
> Energy and Environment Directorate
> Pacific Northwest National Laboratory
> 902 Battelle Boulevard
> P.O. Box 999, MSIN P8-60
> Richland, WA  99352 USA
>
> _______________________________________________
> maker-devel mailing list
> [hidden email]://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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