[maker-devel] Problem with re-annotation

[Carson Holt]

I’m not an expert at all the details in the raw HMM, but it looks like all
your transition probabilities are 0.  You need to regenerate the HMM.  How
many models were used to generate the original HMM?

—Carson


From:  Sanea Sheikh <saneasheikh at gmail.com>
Date:  Saturday, January 18, 2014 at 12:19 AM
To:  Carson Holt <carsonhh at gmail.com>
Cc:  <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] Problem with re-annotation

Hello

Here are the files (test.zip) I got from running Maker again with another
HMM. It clearly worked this time. I have attached my HMM (run0.hmm) from the
previous run (that went wrong) as well. I can see why snap wasn't calling
genes before based on this HMM but do you know why I got an HMM like that?

Sanea


On Fri, Jan 17, 2014 at 10:34 PM, Carson Holt <carsonhh at gmail.com> wrote:
> 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_red
>> undant_remove_130708.maker.output/AR_Hybrid_X2k_Y33_Z200_redundant_remove_130
>> 708_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_red
>> undant_remove_130708.maker.output/AR_Hybrid_X2k_Y33_Z200_redundant_remove_130
>> 708_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.comhttp://box290.bluehost.com/mailman/listinfo/m
>>> aker-devel_yandell-lab.org
>> 
>> 
> 



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