[maker-devel] Problem with re-annotation

[Carson Holt]

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_re
dundant_remove_130708.maker.output/AR_Hybrid_X2k_Y33_Z200_redundant_remove_1
30708_datastore/71/F8/AR_HYBRID_130113_TINTIN_EF2ON_C1/theVoid.AR_HYBRID_130
113_TINTIN_EF2ON_C1/AR_HYBRID_130113_TINTIN_EF2ON_C1.abinit_masked.0.run0%2E
hmm.snap


Second file —>
/gulo/glob/saneash/acrasis_makerv2.28/run1/re-run0/AR_Hybrid_X2k_Y33_Z200_re
dundant_remove_130708.maker.output/AR_Hybrid_X2k_Y33_Z200_redundant_remove_1
30708_datastore/71/F8/AR_HYBRID_130113_TINTIN_EF2ON_C1/AR_HYBRID_130113_TINT
IN_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.comhttp://box290.bluehost.com/mailman/listinfo/mak
> er-devel_yandell-lab.org




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