[maker-devel] Problem with re-annotation

[Sanea Sheikh]

Hi

Here are the two files that you asked for.

The log was from a repeated attempt but the same issue was still there. I
have attached the output from the repeated attempt as well so you can have
a look at that.

Sanea


On Fri, Jan 17, 2014 at 6:55 PM, Carson Holt <carsonhh at gmail.com> wrote:

> Could you send me these two files.  I put the full path below based on
> your STDERR report.  Also this log was from the original run having the
> issue, and not a new repeated attempt at that one, correct?
>
>
> First file —>
>
> /gulo/glob/saneash/acrasis_makerv2.28/run1/re-run0/AR_Hybrid_X2k_Y33_Z200_redundant_remove_130708.maker.output/AR_Hybrid_X2k_Y33_Z200_redundant_remove_130708_datastore/71/F8/AR_HYBRID_130113_TINTIN_EF2ON_C1/theVoid.AR_HYBRID_130113_TINTIN_EF2ON_C1/AR_HYBRID_130113_TINTIN_EF2ON_C1.abinit_masked.0.run0%2Ehmm.snap
>
>
> Second file —>
>
> /gulo/glob/saneash/acrasis_makerv2.28/run1/re-run0/AR_Hybrid_X2k_Y33_Z200_redundant_remove_130708.maker.output/AR_Hybrid_X2k_Y33_Z200_redundant_remove_130708_datastore/71/F8/AR_HYBRID_130113_TINTIN_EF2ON_C1/
> AR_HYBRID_130113_TINTIN_EF2ON_C1.gff
>
>
> Thanks,
> Carson
>
>
> From: Sanea Sheikh <saneasheikh at gmail.com>
> Date: Thursday, January 16, 2014 at 3:52 AM
> To: <maker-devel at yandell-lab.org>, Carson Holt <carsonhh at gmail.com>
> Subject: Fwd: [maker-devel] Problem with re-annotation
>
> Hello Carson
> Here it is.
> Sanea
>
> On Tue, Jan 14, 2014 at 1:39 AM, Carson Holt <carsonhh at gmail.com> wrote:
>
>> Hi Sanea,
>>
>> There are no snap calls in your results.  It’s as if SNAP never even ran.
>>  Did you capture STDERR from your second run?  If so can you send it to me.
>>  I just want to see if it even shows SNAP as having run in the progress
>> reports.
>>
>> Thanks,
>> Carson
>>
>> From: Sanea Sheikh <saneasheikh at gmail.com>
>> Date: Monday, January 13, 2014 at 2:17 AM
>> To: <maker-devel at yandell-lab.org>
>> Subject: [maker-devel] Problem with re-annotation
>>
>> Hello
>>
>> I am using Maker to annotate a genome for which I only have EST data and
>> some protein data. I ran Maker once using this EST and protein data
>> (est2genome=1, protein2genome=1). I had the Maker output. I combined all
>> the GFF files for all the contigs. I used the combined GFF file to train
>> SNAP which gave me a .hmm file. Now I modified the Maker opts control file.
>> I provided the hmm file in snap_hmm. I set est2genome=0 and
>> protein2genome=0. I ran Maker again assuming that now I have trained the
>> gene predictor and I would have better annotations. But now the output file
>> that I get does not have Maker annotation. I have attached the control
>> files and the output file for the re-run so you can have a look and let me
>> know what I am doing wrong in order to re-annotate the genome using the
>> output from the previous run.
>>
>> Sanea
>> _______________________________________________ maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>
>
>
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