[maker-devel] Problem with re-annotation

[Sanea Sheikh]

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_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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