[maker-devel] tutorial: fathom errors: gene:misordered_Einit gene:misordered_Eterm

[Collett, James R]

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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[Carson Holt]

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

[Barry Moore]

Ian,

Could you weigh in on this one?

B

Barry Moore

Research Scientist

Dept. of Human Genetics

University of Utah

Salt Lake City, UT 84112

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