tutorial: fathom errors: gene:misordered_Einit gene:misordered_Eterm

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tutorial: fathom errors: gene:misordered_Einit gene:misordered_Eterm

Collett, James R-2
I'm working through the GMOD Maker tutorial, using my own data for the first time.

I first successfully ran maker with only a transcripts file and a proteins file and generated gff files for about 1000 contigs.  I then ran maker2zff.pl and successfully generated genome.ann and genome.dna files.

I then proceeded with the steps to generate an HMM file for SNAP. When I run fathom, however, I get the following error:

$ fathom -categorize 1000 genome.ann genome.dna
MODEL5113 1 1 3 - errors(2): gene:misordered_Einit gene:misordered_Eterm

Nonetheless, fathom seemed to run to completion, and generated the following files:

$ ls -l
total 53940
-rw-rw-r--. 1 vmuser1 vmuser1      194 Jan 25 15:08 alt.ann
-rw-rw-r--. 1 vmuser1 vmuser1     5904 Jan 25 15:08 alt.dna
-rw-rw-r--. 1 vmuser1 vmuser1        0 Jan 25 15:08 err.ann
-rw-rw-r--. 1 vmuser1 vmuser1        0 Jan 25 15:08 err.dna
-rw-rw-r--. 1 vmuser1 vmuser1   619603 Jan 25 14:56 genome.ann
-rw-rw-r--. 1 vmuser1 vmuser1 32231171 Jan 25 14:56 genome.dna
-rw-rw-r--. 1 vmuser1 vmuser1        0 Jan 25 15:08 olp.ann
-rw-rw-r--. 1 vmuser1 vmuser1        0 Jan 25 15:08 olp.dna
-rw-rw-r--. 1 vmuser1 vmuser1   636423 Jan 25 15:08 uni.ann
-rw-rw-r--. 1 vmuser1 vmuser1 17253260 Jan 25 15:08 uni.dna
-rw-rw-r--. 1 vmuser1 vmuser1   162657 Jan 25 15:08 wrn.ann
-rw-rw-r--. 1 vmuser1 vmuser1  4306505 Jan 25 15:08 wrn.dna

Are these errors something that I should worry about, or should I just go ahead on the next step in the tutorial generating the HMM file, which is:
fathom -export 1000 -plus uni.ann uni.dna ?

Thanks,

Jim


__________________________________________________
James R. Collett, Ph.D.
Senior Scientist
Chemical and Biological Process Development Group
Energy and Environment Directorate
Pacific Northwest National Laboratory


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Re: tutorial: fathom errors: gene:misordered_Einit gene:misordered_Eterm

Carson Holt-2
The error is not an error in the program, but rather a warning about a
non-canonical feature of a gene model.  Fathom suggests that you remove
MODEL5113 before training, but you don't have to if you don't want to.
You can do this by opening up the genome.ann file and just deleting it.
Take a look at the README file that comes with SNAP for more details.

Thanks,
Carson




On 12-01-25 6:48 PM, "Collett, James R" <[hidden email]> wrote:

>I'm working through the GMOD Maker tutorial, using my own data for the
>first time.
>
>I first successfully ran maker with only a transcripts file and a
>proteins file and generated gff files for about 1000 contigs.  I then ran
>maker2zff.pl and successfully generated genome.ann and genome.dna files.
>
>I then proceeded with the steps to generate an HMM file for SNAP. When I
>run fathom, however, I get the following error:
>
>$ fathom -categorize 1000 genome.ann genome.dna
>MODEL5113 1 1 3 - errors(2): gene:misordered_Einit gene:misordered_Eterm
>
>Nonetheless, fathom seemed to run to completion, and generated the
>following files:
>
>$ ls -l
>total 53940
>-rw-rw-r--. 1 vmuser1 vmuser1      194 Jan 25 15:08 alt.ann
>-rw-rw-r--. 1 vmuser1 vmuser1     5904 Jan 25 15:08 alt.dna
>-rw-rw-r--. 1 vmuser1 vmuser1        0 Jan 25 15:08 err.ann
>-rw-rw-r--. 1 vmuser1 vmuser1        0 Jan 25 15:08 err.dna
>-rw-rw-r--. 1 vmuser1 vmuser1   619603 Jan 25 14:56 genome.ann
>-rw-rw-r--. 1 vmuser1 vmuser1 32231171 Jan 25 14:56 genome.dna
>-rw-rw-r--. 1 vmuser1 vmuser1        0 Jan 25 15:08 olp.ann
>-rw-rw-r--. 1 vmuser1 vmuser1        0 Jan 25 15:08 olp.dna
>-rw-rw-r--. 1 vmuser1 vmuser1   636423 Jan 25 15:08 uni.ann
>-rw-rw-r--. 1 vmuser1 vmuser1 17253260 Jan 25 15:08 uni.dna
>-rw-rw-r--. 1 vmuser1 vmuser1   162657 Jan 25 15:08 wrn.ann
>-rw-rw-r--. 1 vmuser1 vmuser1  4306505 Jan 25 15:08 wrn.dna
>
>Are these errors something that I should worry about, or should I just go
>ahead on the next step in the tutorial generating the HMM file, which is:
>fathom -export 1000 -plus uni.ann uni.dna ?
>
>Thanks,
>
>Jim
>
>
>__________________________________________________
>James R. Collett, Ph.D.
>Senior Scientist
>Chemical and Biological Process Development Group
>Energy and Environment Directorate
>Pacific Northwest National Laboratory
>
>
>_______________________________________________
>maker-devel mailing list
>[hidden email]
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org



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Re: tutorial: fathom errors: gene:misordered_Einit gene:misordered_Eterm

Marvin B Moore
In reply to this post by Collett, James R-2
Ian,

Could you weigh in on this one?

B

On Jan 25, 2012, at 4:48 PM, Collett, James R wrote:

I'm working through the GMOD Maker tutorial, using my own data for the first time.

I first successfully ran maker with only a transcripts file and a proteins file and generated gff files for about 1000 contigs.  I then ran maker2zff.pl and successfully generated genome.ann and genome.dna files.

I then proceeded with the steps to generate an HMM file for SNAP. When I run fathom, however, I get the following error:

$ fathom -categorize 1000 genome.ann genome.dna
MODEL5113 1 1 3 - errors(2): gene:misordered_Einit gene:misordered_Eterm

Nonetheless, fathom seemed to run to completion, and generated the following files:

$ ls -l
total 53940
-rw-rw-r--. 1 vmuser1 vmuser1      194 Jan 25 15:08 alt.ann
-rw-rw-r--. 1 vmuser1 vmuser1     5904 Jan 25 15:08 alt.dna
-rw-rw-r--. 1 vmuser1 vmuser1        0 Jan 25 15:08 err.ann
-rw-rw-r--. 1 vmuser1 vmuser1        0 Jan 25 15:08 err.dna
-rw-rw-r--. 1 vmuser1 vmuser1   619603 Jan 25 14:56 genome.ann
-rw-rw-r--. 1 vmuser1 vmuser1 32231171 Jan 25 14:56 genome.dna
-rw-rw-r--. 1 vmuser1 vmuser1        0 Jan 25 15:08 olp.ann
-rw-rw-r--. 1 vmuser1 vmuser1        0 Jan 25 15:08 olp.dna
-rw-rw-r--. 1 vmuser1 vmuser1   636423 Jan 25 15:08 uni.ann
-rw-rw-r--. 1 vmuser1 vmuser1 17253260 Jan 25 15:08 uni.dna
-rw-rw-r--. 1 vmuser1 vmuser1   162657 Jan 25 15:08 wrn.ann
-rw-rw-r--. 1 vmuser1 vmuser1  4306505 Jan 25 15:08 wrn.dna

Are these errors something that I should worry about, or should I just go ahead on the next step in the tutorial generating the HMM file, which is:
fathom -export 1000 -plus uni.ann uni.dna ?

Thanks,

Jim


__________________________________________________
James R. Collett, Ph.D.
Senior Scientist
Chemical and Biological Process Development Group
Energy and Environment Directorate
Pacific Northwest National Laboratory


_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543





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