gene:multiple_Einit and overlaps_prev_exon errors in first round of SNAP training

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gene:multiple_Einit and overlaps_prev_exon errors in first round of SNAP training

Carneiro,Celine M
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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Re: gene:multiple_Einit and overlaps_prev_exon errors in first round of SNAP training

Carson Holt-2
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 <[hidden email]> 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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maker-devel mailing list
[hidden email]
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_______________________________________________
maker-devel mailing list
[hidden email]
http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org