[maker-devel] gene:multiple_Einit and overlaps_prev_exon errors in first round of SNAP training

Carson Holt carsonhh at gmail.com
Tue May 26 13:15:20 MDT 2020 

You have an ID collision in the GFF3.  Check the gff3 being sent to maker2zff. If you are using GFF3 as input to MAKER, you likely have a non-unique ID's there that are causing the issue in the first place.

—Carson





> On May 6, 2020, at 11:36 AM, Carneiro,Celine M <c143dad at ufl.edu> wrote:
> 
> Hello,
> 
> I am getting the errors gene:multiple_Einit, gene:multiple_Eterm, and exon:overlaps_prev_exon, at just about every gene model. I've ran the first round of maker on a bird genome I'm annotating with no errors and have started the steps to train SNAP. However, after running fathom -categorize, just about every single gene model has the same set of errors. Here is an example from my log file after running fathom -categorize:
> 
> MODEL117 1 1 8 - errors(6): gene:multiple_Einit gene:multiple_Eterm exon-7:overlaps_prev_exon exon-5:overlaps_prev_exon exon-3:overlaps_prev_exon exon-1:overlaps_prev_exon
> MODEL851 1 1 100 - errors(78): gene:multiple_Einit gene:multiple_Eterm exon-99:overlaps_prev_exon exon-98:overlaps_prev_exon exon-97:overlaps_prev_exon exon-95:overlaps_prev_exon exon-94:overlaps_prev_exon exon-93:overlaps_prev_exon exon-91:overlaps_prev_exon exon-90:overlaps_prev_exon exon-89:overlaps_prev_exon exon-87:overlaps_prev_exon exon-86:overlaps_prev_exon exon-85:overlaps_prev_exon exon-83:overlaps_prev_exon exon-82:overlaps_prev_exon exon-81:overlaps_prev_exon exon-79:overlaps_prev_exon exon-78:overlaps_prev_exon exon-77:overlaps_prev_exon exon-75:overlaps_prev_exon exon-74:overlaps_prev_exon exon-73:overlaps_prev_exon exon-71:overlaps_prev_exon exon-70:overlaps_prev_exon exon-69:overlaps_prev_exon exon-67:overlaps_prev_exon exon-66:overlaps_prev_exon exon-65:overlaps_prev_exon exon-63:overlaps_prev_exon exon-62:overlaps_prev_exon exon-61:overlaps_prev_exon exon-59:overlaps_prev_exon exon-58:overlaps_prev_exon exon-57:overlaps_prev_exon exon-55:overlaps_prev_exon exon-54:overlaps_prev_exon exon-53:overlaps_prev_exon exon-51:overlaps_prev_exon exon-50:overlaps_prev_exon exon-49:overlaps_prev_exon exon-48:overlaps_prev_exon exon-47:overlaps_prev_exon exon-46:overlaps_prev_exon exon-45:overlaps_prev_exon exon-43:overlaps_prev_exon exon-42:overlaps_prev_exon exon-41:overlaps_prev_exon exon-39:overlaps_prev_exon exon-38:overlaps_prev_exon exon-37:overlaps_prev_exon exon-35:overlaps_prev_exon exon-34:overlaps_prev_exon exon-33:overlaps_prev_exon exon-31:overlaps_prev_exon exon-30:overlaps_prev_exon exon-29:overlaps_prev_exon exon-27:overlaps_prev_exon exon-26:overlaps_prev_exon exon-25:overlaps_prev_exon exon-23:overlaps_prev_exon exon-22:overlaps_prev_exon exon-21:overlaps_prev_exon exon-19:overlaps_prev_exon exon-18:overlaps_prev_exon exon-17:overlaps_prev_exon exon-15:overlaps_prev_exon exon-14:overlaps_prev_exon exon-13:overlaps_prev_exon exon-11:overlaps_prev_exon exon-10:overlaps_prev_exon exon-9:overlaps_prev_exon exon-7:overlaps_prev_exon exon-6:overlaps_prev_exon exon-5:overlaps_prev_exon exon-3:overlaps_prev_exon exon-2:overlaps_prev_exon exon-1:overlaps_prev_exon
> MODEL190 1 1 39 + errors(35): gene:multiple_Einit gene:multiple_Eterm exon-2:overlaps_prev_exon exon-3:overlaps_prev_exon exon-4:overlaps_prev_exon exon-5:overlaps_prev_exon exon-6:overlaps_prev_exon exon-7:overlaps_prev_exon exon-8:overlaps_prev_exon exon-9:overlaps_prev_exon exon-11:overlaps_prev_exon exon-12:overlaps_prev_exon exon-13:overlaps_prev_exon exon-14:overlaps_prev_exon exon-15:overlaps_prev_exon exon-16:overlaps_prev_exon exon-17:overlaps_prev_exon exon-18:overlaps_prev_exon exon-20:overlaps_prev_exon exon-21:overlaps_prev_exon exon-22:overlaps_prev_exon exon-23:overlaps_prev_exon exon-24:overlaps_prev_exon exon-25:overlaps_prev_exon exon-26:overlaps_prev_exon exon-27:overlaps_prev_exon exon-29:overlaps_prev_exon exon-30:overlaps_prev_exon exon-32:overlaps_prev_exon exon-33:overlaps_prev_exon exon-34:overlaps_prev_exon exon-35:overlaps_prev_exon exon-36:overlaps_prev_exon exon-38:overlaps_prev_exon exon-39:overlaps_prev_exon
> MODEL424 1 1 10 - errors(8): gene:multiple_Einit gene:multiple_Eterm exon-9:overlaps_prev_exon exon-7:overlaps_prev_exon exon-6:overlaps_prev_exon exon-5:overlaps_prev_exon exon-3:overlaps_prev_exon exon-1:overlaps_prev_exon
> MODEL902 1 1 20 - errors(14): gene:multiple_Einit gene:multiple_Eterm exon-19:overlaps_prev_exon exon-18:overlaps_prev_exon exon-17:overlaps_prev_exon exon-15:overlaps_prev_exon exon-13:overlaps_prev_exon exon-11:overlaps_prev_exon exon-9:overlaps_prev_exon exon-7:overlaps_prev_exon exon-6:overlaps_prev_exon exon-5:overlaps_prev_exon exon-3:overlaps_prev_exon exon-1:overlaps_prev_exon
> MODEL238 1 1 14 - errors(11): gene:multiple_Einit gene:multiple_Eterm exon-13:overlaps_prev_exon exon-12:overlaps_prev_exon exon-11:overlaps_prev_exon exon-9:overlaps_prev_exon exon-7:overlaps_prev_exon exon-6:overlaps_prev_exon exon-5:overlaps_prev_exon exon-3:overlaps_prev_exon exon-1:overlaps_prev_exon
> MODEL39 1 1 6 - errors(1): exon-3:overlaps_prev_exon
> MODEL119 1 1 10 + errors(8): gene:multiple_Einit gene:multiple_Eterm exon-2:overlaps_prev_exon exon-4:overlaps_prev_exon exon-6:overlaps_prev_exon exon-7:overlaps_prev_exon exon-8:overlaps_prev_exon exon-10:overlaps_prev_exon
> 
> Furthermore, I checked my genome.ann file and noticed that my Einit and Exon sites are duplicated. For example:
> 
> >ScdimlH_1004;HRSCAF=1084
> Einit  38730 38677 MODEL851
> Exon  38255 38178 MODEL851
> Exon  38074 38021 MODEL851
> Exon  24755 24717 MODEL851
> Exon  24213 24149 MODEL851
> Exon  23176 23098 MODEL851
> Exon  22037 21961 MODEL851
> Exon  21269 21080 MODEL851
> Exon  20232 20167 MODEL851
> Exon  19742 19704 MODEL851
> Exon  14705 14590 MODEL851
> Exon  14255 13980 MODEL851
> Exon  14169 13980 MODEL851
> Exon  13303 13223 MODEL851
> Exon  13303 13223 MODEL851
> Exon  12782 12639 MODEL851
> Exon  12782 12639 MODEL851
> Exon  5761 5592 MODEL851
> Exon  5482 5404 MODEL851
> Exon  5140 5064 MODEL851
> Exon  4951 4750 MODEL851
> Exon  4567 4502 MODEL851
> Exon  4256 4185 MODEL851
> Exon  3569 3403 MODEL851
> Exon  3157 3076 MODEL851
> Exon  2936 2800 MODEL851
> Eterm  2186 2000 MODEL851
> Einit  38730 38677 MODEL851
> Exon  38255 38178 MODEL851
> Exon  38074 38021 MODEL851
> Exon  24755 24717 MODEL851
> Exon  24213 24149 MODEL851
> Exon  23176 23098 MODEL851
> Exon  22037 21961 MODEL851
> Exon  21269 21080 MODEL851
> Exon  20232 20167 MODEL851
> Exon  19742 19704 MODEL851
> Exon  14705 14590 MODEL851
> Exon  14255 13980 MODEL851
> Exon  14169 13980 MODEL851
> Exon  13303 13223 MODEL851
> Exon  13303 13223 MODEL851
> Exon  12782 12639 MODEL851
> Exon  12782 12639 MODEL851
> Exon  5761 5592 MODEL851
> Exon  5482 5404 MODEL851
> Exon  5140 5064 MODEL851
> Exon  4951 4750 MODEL851
> Exon  4567 4502 MODEL851
> Exon  4256 4185 MODEL851
> Exon  3569 3403 MODEL851
> Exon  3157 3076 MODEL851
> Exon  2936 2800 MODEL851
> Eterm  2186 2000 MODEL851
> 
> Any ideas why I'm seeing this duplication? Lastly, any ideas why my exons are overlapping so much? I appreciate any input and please let me know if you require any more information. 
> 
> Thank you!
> 
> Celine
> 
> 
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