-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_20/scaffold_20_3039212-3249615

-reading genomic sequence.

** Processing features (+)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: +)
-loading gene prediction evidence. (strand: +)Valid prediction for GeneMark_model.81556_t
Valid prediction for GlimmerHMM_glimmerT_46808-T1
Valid prediction for GeneMark_model.81553_t
Valid prediction for Augustus_model.g31252.t1
Valid prediction for Augustus_model.g31250.t1
Valid prediction for Augustus_model.g31243.t1
Valid prediction for snap_scaffold_20-snap.678-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for HiQ_model.g31253.t1
Valid prediction for GlimmerHMM_glimmerT_46795-T1
Valid prediction for GeneMark_model.81564_t
Valid prediction for GeneMark_model.81579_t
Valid prediction for GeneMark_model.81624_t
Valid prediction for GeneMark_model.81584_t
Valid prediction for snap_scaffold_20-snap.695-T1
Valid prediction for GeneMark_model.81565_t
Valid prediction for GlimmerHMM_glimmerT_46806-T1
Valid prediction for GlimmerHMM_glimmerT_46803-T1
Valid prediction for GeneMark_model.81580_t
Valid prediction for GlimmerHMM_glimmerT_46801-T1
Valid prediction for GlimmerHMM_glimmerT_46789-T1
Valid prediction for GeneMark_model.81607_t
Valid prediction for Augustus_model.g31244.t1
Valid prediction for GeneMark_model.81615_t
Valid prediction for GlimmerHMM_glimmerT_46787-T1
Valid prediction for GeneMark_model.81551_t
Valid prediction for Augustus_model.g31247.t1
Valid prediction for GeneMark_model.81543_t
Valid prediction for snap_scaffold_20-snap.662-T1
Valid prediction for GeneMark_model.81598_t
Valid prediction for GeneMark_model.81586_t
Valid prediction for GeneMark_model.81560_t
Valid prediction for snap_scaffold_20-snap.699-T1
Valid prediction for GeneMark_model.81594_t
Valid prediction for Augustus_model.g31251.t1
Valid prediction for snap_scaffold_20-snap.668-T1
Valid prediction for GlimmerHMM_glimmerT_46793-T1
Valid prediction for GeneMark_model.81567_t
Valid prediction for snap_scaffold_20-snap.663-T1
Valid prediction for GlimmerHMM_glimmerT_46804-T1
Valid prediction for GlimmerHMM_glimmerT_46790-T1
Valid prediction for snap_scaffold_20-snap.669-T1
Valid prediction for snap_scaffold_20-snap.701-T1
Valid prediction for GeneMark_model.81609_t
Valid prediction for GeneMark_model.81600_t
Valid prediction for GeneMark_model.81588_t
Valid prediction for GeneMark_model.81582_t
Valid prediction for GeneMark_model.81575_t
Couldn't classify 25330, 25427
Couldn't classify 27015, 27100
Sorry, prediction pasa_asmbl_26313.p2 fails validation.
(AAC)	 AC	25330-25427	GT	AGG
(AGA)	 AG	25706-25786	GT	AGG
(ACA)	 AG	26406-26518	GT	AGG
(ACA)	 AG	27015-27100	CG	AAC
-recovered pasa_asmbl_26313.p2, internal, 25706, 25786
-recovered pasa_asmbl_26313.p2, internal, 26406, 26518
Valid prediction for snap_scaffold_20-snap.677-T1
Valid prediction for snap_scaffold_20-snap.696-T1
Valid prediction for snap_scaffold_20-snap.664-T1
Valid prediction for GeneMark_model.81602_t
Valid prediction for GeneMark_model.81612_t
Valid prediction for GlimmerHMM_glimmerT_46805-T1
Valid prediction for Augustus_model.g31255.t1
Valid prediction for GeneMark_model.81568_t
Valid prediction for CodingQuarry_transcript_30416-T1
Valid prediction for snap_scaffold_20-snap.694-T1
Valid prediction for GeneMark_model.81605_t
Valid prediction for GeneMark_model.81550_t
Valid prediction for GeneMark_model.81581_t
Valid prediction for GeneMark_model.81573_t
Valid prediction for snap_scaffold_20-snap.672-T1
Valid prediction for snap_scaffold_20-snap.700-T1
Valid prediction for Augustus_model.g31249.t1
Valid prediction for GeneMark_model.81613_t
Valid prediction for GeneMark_model.81629_t
Valid prediction for snap_scaffold_20-snap.666-T1
Valid prediction for snap_scaffold_20-snap.661-T1
Valid prediction for GeneMark_model.81620_t
Valid prediction for GeneMark_model.81577_t
Valid prediction for GeneMark_model.81562_t
Valid prediction for GeneMark_model.81547_t
Valid prediction for GeneMark_model.81569_t
Valid prediction for GeneMark_model.81542_t
Valid prediction for snap_scaffold_20-snap.682-T1
Valid prediction for snap_scaffold_20-snap.685-T1
Valid prediction for GeneMark_model.81628_t
Valid prediction for GlimmerHMM_glimmerT_46799-T1
Valid prediction for GeneMark_model.81622_t
Valid prediction for snap_scaffold_20-snap.676-T1
Valid prediction for pasa_asmbl_25673.p1
Valid prediction for GlimmerHMM_glimmerT_46798-T1
Valid prediction for GeneMark_model.81571_t
Valid prediction for GeneMark_model.81544_t
Valid prediction for Augustus_model.g31248.t1
Valid prediction for GlimmerHMM_glimmerT_46800-T1
Valid prediction for GeneMark_model.81558_t
Valid prediction for GeneMark_model.81548_t
Valid prediction for GeneMark_model.81617_t
Valid prediction for GeneMark_model.81626_t

-loading the search evidence (protein and EST search results, strand: +)
-scoring exons (strand: +)

** Processing features (-)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: -)
-loading gene prediction evidence. (strand: -)Valid prediction for GlimmerHMM_glimmerT_46788-T1
Valid prediction for GeneMark_model.81589_t
Valid prediction for GlimmerHMM_glimmerT_46794-T1
Valid prediction for snap_scaffold_20-snap.660-T1
Valid prediction for snap_scaffold_20-snap.686-T1
Valid prediction for GeneMark_model.81557_t
Valid prediction for GlimmerHMM_glimmerT_46791-T1
Valid prediction for snap_scaffold_20-snap.690-T1
Valid prediction for GeneMark_model.81549_t
Valid prediction for GeneMark_model.81572_t
Valid prediction for GeneMark_model.81603_t
Valid prediction for GeneMark_model.81599_t
Valid prediction for GlimmerHMM_glimmerT_46796-T1
Valid prediction for snap_scaffold_20-snap.684-T1
Valid prediction for Augustus_model.g31254.t1
Valid prediction for snap_scaffold_20-snap.698-T1
Valid prediction for snap_scaffold_20-snap.697-T1
Valid prediction for GeneMark_model.81596_t
Valid prediction for GeneMark_model.81563_t
Valid prediction for GeneMark_model.81606_t
Valid prediction for snap_scaffold_20-snap.679-T1
Valid prediction for GeneMark_model.81552_t
Valid prediction for GeneMark_model.81604_t
Valid prediction for GeneMark_model.81561_t
Valid prediction for GeneMark_model.81554_t
Valid prediction for GeneMark_model.81608_t
Valid prediction for Augustus_model.g31242.t1
Valid prediction for snap_scaffold_20-snap.674-T1
Valid prediction for Augustus_model.g31245.t1
Valid prediction for GeneMark_model.81614_t
Valid prediction for GlimmerHMM_glimmerT_46797-T1
Valid prediction for GeneMark_model.81618_t
Valid prediction for GeneMark_model.81541_t
Valid prediction for GeneMark_model.81623_t
Valid prediction for snap_scaffold_20-snap.667-T1
Valid prediction for GlimmerHMM_glimmerT_46786-T1
Couldn't classify 169925, 170071
Couldn't classify 170410, 170574
Sorry, prediction pasa_asmbl_27177.p1 fails validation.
(GTA)	 CA	169925-170071	GT	AGG
(CCC)	 AG	170410-170574	AA	CCA
Valid prediction for snap_scaffold_20-snap.687-T1
Valid prediction for GeneMark_model.81583_t
Valid prediction for GeneMark_model.81616_t
Valid prediction for GeneMark_model.81555_t
Valid prediction for GeneMark_model.81591_t
Valid prediction for GeneMark_model.81585_t
Valid prediction for snap_scaffold_20-snap.693-T1
Valid prediction for snap_scaffold_20-snap.683-T1
Valid prediction for GeneMark_model.81559_t
Valid prediction for snap_scaffold_20-snap.673-T1
Valid prediction for GeneMark_model.81545_t
Valid prediction for GeneMark_model.81570_t
Valid prediction for GeneMark_model.81619_t
Valid prediction for GeneMark_model.81621_t
Valid prediction for snap_scaffold_20-snap.688-T1
Valid prediction for GeneMark_model.81578_t
Valid prediction for snap_scaffold_20-snap.680-T1
Valid prediction for GeneMark_model.81601_t
Valid prediction for GeneMark_model.81611_t
Valid prediction for GeneMark_model.81625_t
Valid prediction for snap_scaffold_20-snap.691-T1
Valid prediction for GeneMark_model.81610_t
Valid prediction for GlimmerHMM_glimmerT_46802-T1
Valid prediction for snap_scaffold_20-snap.692-T1
Valid prediction for GeneMark_model.81574_t
Valid prediction for GeneMark_model.81566_t
Valid prediction for snap_scaffold_20-snap.671-T1
Couldn't classify 79776, 79874
Sorry, prediction GeneMark_model.81592_t fails validation.
(ATG)	 AC	79207-79256	GT	GAG
(AGG)	 AG	79283-79414	GT	GTG
(GGA)	 AG	79452-79469	GT	CTG
(AGG)	 AG	79500-79505	GT	GGG
(TAG)	 AG	79530-79538	GT	GGG
(AGG)	 AG	79616-79690	GT	TGG
(GAG)	 AG	79720-79752	GT	GGG
(AAA)	 AG	79776-79874	GT	TGG
-recovered GeneMark_model.81592_t, initial, 79207, 79256
-recovered GeneMark_model.81592_t, internal, 79283, 79414
-recovered GeneMark_model.81592_t, internal, 79452, 79469
-recovered GeneMark_model.81592_t, internal, 79500, 79505
-recovered GeneMark_model.81592_t, internal, 79530, 79538
-recovered GeneMark_model.81592_t, internal, 79616, 79690
-recovered GeneMark_model.81592_t, internal, 79720, 79752
-recovered GeneMark_model.81592_t, internal, 79776, 79874
Valid prediction for GeneMark_model.81627_t
Valid prediction for GlimmerHMM_glimmerT_46807-T1
Valid prediction for snap_scaffold_20-snap.681-T1
Valid prediction for snap_scaffold_20-snap.689-T1
Valid prediction for Augustus_model.g31246.t1
Valid prediction for GeneMark_model.81597_t
Valid prediction for snap_scaffold_20-snap.675-T1
Valid prediction for GeneMark_model.81593_t
Valid prediction for GeneMark_model.81546_t
Valid prediction for snap_scaffold_20-snap.670-T1
Valid prediction for snap_scaffold_20-snap.665-T1
Valid prediction for GlimmerHMM_glimmerT_46792-T1
Valid prediction for GeneMark_model.81595_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10806, rend_intergenic: 3171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27235, rend_intergenic: 21285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33833, rend_intergenic: 27519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38667, rend_intergenic: 35308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48488, rend_intergenic: 39593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51732, rend_intergenic: 48986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53863, rend_intergenic: 52560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82438, rend_intergenic: 74683  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131320, rend_intergenic: 82695  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138233, rend_intergenic: 132924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139654, rend_intergenic: 138617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171489, rend_intergenic: 139883  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178429, rend_intergenic: 175435  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191621, rend_intergenic: 189566  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207634, rend_intergenic: 196061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 210404
-exon list size: 1020


building trellis

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61.1    
61.2    
61.3    
61.4    
61.4    
61.5    
61.6    
61.7    
61.8    
61.9    
62.0    
62.1    
62.2    
62.3    
62.4    
62.5    
62.6    
62.7    
62.8    
62.9    
63.0    
63.1    
63.2    
63.3    
63.4    
63.5    
63.6    
63.7    
63.8    
63.9    
64.0    
64.1    
64.2    
64.3    
64.4    
64.5    
64.6    
64.7    
64.8    
64.9    
65.0    
65.1    
65.2    
65.3    
65.4    
65.5    
65.6    
65.7    
65.8    
65.9    
65.9    
66.0    
66.1    
66.2    
66.3    
66.4    
66.5    
66.6    
66.7    
66.8    
66.9    
67.0    
67.1    
67.2    
67.3    
67.4    
67.5    
67.6    
67.7    
67.8    
67.9    
68.0    
68.1    
68.2    
68.3    
68.4    
68.5    
68.6    
68.7    
68.8    
68.9    
69.0    
69.1    
69.2    
69.3    
69.4    
69.5    
69.6    
69.7    
69.8    
69.9    
70.0    
70.1    
70.2    
70.3    
70.4    
70.5    
70.5    
70.6    
70.7    
70.8    
70.9    
71.0    
71.1    
71.2    
71.3    
71.4    
71.5    
71.6    
71.7    
71.8    
71.9    
72.0    
72.1    
72.2    
72.3    
72.4    
72.5    
72.6    
72.7    
72.8    
72.9    
73.0    
73.1    
73.2    
73.3    
73.4    
73.5    
73.6    
73.7    
73.8    
73.9    
74.0    
74.1    
74.2    
74.3    
74.4    
74.5    
74.6    
74.7    
74.8    
74.9    
75.0    
75.0    
75.1    
75.2    
75.3    
75.4    
75.5    
75.6    
75.7    
75.8    
75.9    
76.0    
76.1    
76.2    
76.3    
76.4    
76.5    
76.6    
76.7    
76.8    
76.9    
77.0    
77.1    
77.2    
77.3    
77.4    
77.5    
77.6    
77.7    
77.8    
77.9    
78.0    
78.1    
78.2    
78.3    
78.4    
78.5    
78.6    
78.7    
78.8    
78.9    
79.0    
79.1    
79.2    
79.3    
79.4    
79.5    
79.5    
79.6    
79.7    
79.8    
79.9    
80.0    
80.1    
80.2    
80.3    
80.4    
80.5    
80.6    
80.7    
80.8    
80.9    
81.0    
81.1    
81.2    
81.3    
81.4    
81.5    
81.6    
81.7    
81.8    
81.9    
82.0    
82.1    
82.2    
82.3    
82.4    
82.5    
82.6    
82.7    
82.8    
82.9    
83.0    
83.1    
83.2    
83.3    
83.4    
83.5    
83.6    
83.7    
83.8    
83.9    
84.0    
84.1    
84.1    
84.2    
84.3    
84.4    
84.5    
84.6    
84.7    
84.8    
84.9    
85.0    
85.1    
85.2    
85.3    
85.4    
85.5    
85.6    
85.7    
85.8    
85.9    
86.0    
86.1    
86.2    
86.3    
86.4    
86.5    
86.6    
86.7    
86.8    
86.9    
87.0    
87.1    
87.2    
87.3    
87.4    
87.5    
87.6    
87.7    
87.8    
87.9    
88.0    
88.1    
88.2    
88.3    
88.4    
88.5    
88.6    
88.6    
88.7    
88.8    
88.9    
89.0    
89.1    
89.2    
89.3    
89.4    
89.5    
89.6    
89.7    
89.8    
89.9    
90.0    
90.1    
90.2    
90.3    
90.4    
90.5    
90.6    
90.7    
90.8    
90.9    
91.0    
91.1    
91.2    
91.3    
91.4    
91.5    
91.6    
91.7    
91.8    
91.9    
92.0    
92.1    
92.2    
92.3    
92.4    
92.5    
92.6    
92.7    
92.8    
92.9    
93.0    
93.1    
93.2    
93.2    
93.3    
93.4    
93.5    
93.6    
93.7    
93.8    
93.9    
94.0    
94.1    
94.2    
94.3    
94.4    
94.5    
94.6    
94.7    
94.8    
94.9    
95.0    
95.1    
95.2    
95.3    
95.4    
95.5    
95.6    
95.7    
95.8    
95.9    
96.0    
96.1    
96.2    
96.3    
96.4    
96.5    
96.6    
96.7    
96.8    
96.9    
97.0    
97.1    
97.2    
97.3    
97.4    
97.5    
97.6    
97.7    
97.7    
97.8    
97.9    
98.0    
98.1    
98.2    
98.3    
98.4    
98.5    
98.6    
98.7    
98.8    
98.9    
99.0    
99.1    
99.2    
99.3    
99.4    
99.5    
99.6    
99.7    
99.8    
99.9    
-found 59 predictions from path traversal
Error with prediction: snap lend_intergenic: 10806, rend_intergenic: 3171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27235, rend_intergenic: 21285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33833, rend_intergenic: 27519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38667, rend_intergenic: 35308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48488, rend_intergenic: 39593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51732, rend_intergenic: 48986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53863, rend_intergenic: 52560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82438, rend_intergenic: 74683  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131320, rend_intergenic: 82695  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138233, rend_intergenic: 132924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139654, rend_intergenic: 138617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171489, rend_intergenic: 139883  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178429, rend_intergenic: 175435  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191621, rend_intergenic: 189566  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207634, rend_intergenic: 196061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support