[maker-devel] Problem with re-annotation

[Carson Holt]

The snap reports are empty, as if SNAP is never calling any genes even
though it runs.  Could you try running with a different HMM bundled with
SNAP? Even though it’s not the right species, I just want to see if it will
produce output under different circumstances.

—Carson


From:  Sanea Sheikh <saneasheikh at gmail.com>
Date:  Friday, January 17, 2014 at 12:21 PM
To:  Carson Holt <carsonhh at gmail.com>
Cc:  <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] Problem with re-annotation

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_redu
> ndant_remove_130708.maker.output/AR_Hybrid_X2k_Y33_Z200_redundant_remove_13070
> 8_datastore/71/F8/AR_HYBRID_130113_TINTIN_EF2ON_C1/theVoid.AR_HYBRID_130113_TI
> NTIN_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_redu
> ndant_remove_130708.maker.output/AR_Hybrid_X2k_Y33_Z200_redundant_remove_13070
> 8_datastore/71/F8/AR_HYBRID_130113_TINTIN_EF2ON_C1/AR_HYBRID_130113_TINTIN_EF2
> ON_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/ma
>> ker-devel_yandell-lab.org
> 
> 



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