-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_7/scaffold_7_13869006-14068631

-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 snap_scaffold_7-snap.2633-T1
Valid prediction for GeneMark_model.31586_t
Valid prediction for GeneMark_model.31575_t
Valid prediction for snap_scaffold_7-snap.2641-T1
Valid prediction for GeneMark_model.31605_t
Valid prediction for GlimmerHMM_glimmerT_18870-T1
Valid prediction for GeneMark_model.31577_t
Valid prediction for pasa_asmbl_51271.p1
Valid prediction for GeneMark_model.31611_t
Valid prediction for snap_scaffold_7-snap.2622-T1
Valid prediction for snap_scaffold_7-snap.2621-T1
Valid prediction for GeneMark_model.31584_t
Valid prediction for pasa_asmbl_51264.p1
Valid prediction for HiQ_model.g12764.t1
Valid prediction for GlimmerHMM_glimmerT_18861-T1
Valid prediction for GeneMark_model.31613_t
Valid prediction for snap_scaffold_7-snap.2626-T1
Valid prediction for CodingQuarry_transcript_57561-T1
Valid prediction for GlimmerHMM_glimmerT_18853-T1
Valid prediction for CodingQuarry_transcript_57562-T1
Valid prediction for GeneMark_model.31619_t
Valid prediction for snap_scaffold_7-snap.2638-T1
Valid prediction for snap_scaffold_7-snap.2642-T1
Valid prediction for GeneMark_model.31582_t
Valid prediction for snap_scaffold_7-snap.2652-T1
Valid prediction for snap_scaffold_7-snap.2644-T1
Valid prediction for GlimmerHMM_glimmerT_18852-T1
Valid prediction for CodingQuarry_transcript_57560-T1
Valid prediction for snap_scaffold_7-snap.2618-T1
Valid prediction for snap_scaffold_7-snap.2619-T1
Valid prediction for GeneMark_model.31580_t
Valid prediction for pasa_asmbl_51275.p1
Valid prediction for snap_scaffold_7-snap.2623-T1
Valid prediction for GlimmerHMM_glimmerT_18862-T1
Valid prediction for snap_scaffold_7-snap.2636-T1
Valid prediction for snap_scaffold_7-snap.2631-T1
Valid prediction for Augustus_model.g12773.t1
Valid prediction for GlimmerHMM_glimmerT_18871-T1
Valid prediction for CodingQuarry_transcript_57565-T1
Valid prediction for snap_scaffold_7-snap.2615-T1
Valid prediction for HiQ_model.g12758.t1
Valid prediction for GeneMark_model.31609_t
Valid prediction for Augustus_model.g12762.t1
Valid prediction for GeneMark_model.31594_t
Valid prediction for snap_scaffold_7-snap.2648-T1
Valid prediction for snap_scaffold_7-snap.2629-T1
Valid prediction for snap_scaffold_7-snap.2655-T1
Valid prediction for snap_scaffold_7-snap.2639-T1
Valid prediction for HiQ_model.g12765.t1
Valid prediction for Augustus_model.g12770.t1
Valid prediction for Augustus_model.g12772.t1
Valid prediction for snap_scaffold_7-snap.2632-T1
Valid prediction for GeneMark_model.31601_t
Valid prediction for CodingQuarry_transcript_57566-T1
Valid prediction for pasa_asmbl_51268.p1
Valid prediction for Augustus_model.g12771.t1
Valid prediction for GeneMark_model.31620_t
Valid prediction for CodingQuarry_transcript_57564-T1
Valid prediction for snap_scaffold_7-snap.2657-T1
Valid prediction for GeneMark_model.31579_t
Valid prediction for snap_scaffold_7-snap.2651-T1
Valid prediction for GlimmerHMM_glimmerT_18860-T1
Valid prediction for snap_scaffold_7-snap.2630-T1
Valid prediction for GlimmerHMM_glimmerT_18865-T1
Valid prediction for GeneMark_model.31615_t
Valid prediction for GeneMark_model.31593_t
Valid prediction for GeneMark_model.31589_t
Valid prediction for GeneMark_model.31603_t
Valid prediction for GlimmerHMM_glimmerT_18858-T1
Valid prediction for snap_scaffold_7-snap.2624-T1
Valid prediction for GeneMark_model.31572_t
Valid prediction for snap_scaffold_7-snap.2627-T1
Couldn't classify 81108, 81158
Sorry, prediction pasa_asmbl_51269.p1 fails validation.
(ATG)	 AT	78315-78433	GT	AAG
(GAA)	 AG	78829-78889	GT	AGG
(CTT)	 AG	79003-79077	GT	TTG
(GTG)	 AG	79387-79492	GT	TGG
(ACA)	 AG	79595-79644	GT	AGG
(GTG)	 AG	79767-79830	GT	AGG
(CGT)	 AG	80137-80184	GT	TGG
(GTG)	 AG	80294-80407	GT	GGG
(TGA)	 AG	80591-80777	GT	CAG
(ATT)	 AG	80871-80922	GT	AGG
(ATC)	 AG	81108-81158	AT	AGA
-recovered pasa_asmbl_51269.p1, initial, 78315, 78433
-recovered pasa_asmbl_51269.p1, internal, 78829, 78889
-recovered pasa_asmbl_51269.p1, internal, 79003, 79077
-recovered pasa_asmbl_51269.p1, internal, 79387, 79492
-recovered pasa_asmbl_51269.p1, internal, 79595, 79644
-recovered pasa_asmbl_51269.p1, internal, 79767, 79830
-recovered pasa_asmbl_51269.p1, internal, 80137, 80184
-recovered pasa_asmbl_51269.p1, internal, 80294, 80407
-recovered pasa_asmbl_51269.p1, internal, 80591, 80777
-recovered pasa_asmbl_51269.p1, internal, 80871, 80922
Valid prediction for CodingQuarry_transcript_57563-T1
Valid prediction for HiQ_model.g12757.t1

-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 GeneMark_model.31616_t
Valid prediction for GlimmerHMM_glimmerT_18866-T1
Valid prediction for GeneMark_model.31597_t
Valid prediction for GlimmerHMM_glimmerT_18868-T1
Valid prediction for snap_scaffold_7-snap.2653-T1
Valid prediction for GeneMark_model.31578_t
Valid prediction for GeneMark_model.31598_t
Valid prediction for Augustus_model.g12761.t1
Valid prediction for snap_scaffold_7-snap.2634-T1
Valid prediction for snap_scaffold_7-snap.2647-T1
Valid prediction for GeneMark_model.31595_t
Valid prediction for GlimmerHMM_glimmerT_18855-T1
Valid prediction for GeneMark_model.31604_t
Valid prediction for GeneMark_model.31585_t
Valid prediction for GeneMark_model.31596_t
Valid prediction for GlimmerHMM_glimmerT_18854-T1
Valid prediction for GeneMark_model.31591_t
Valid prediction for GeneMark_model.31602_t
Valid prediction for GeneMark_model.31606_t
Valid prediction for snap_scaffold_7-snap.2625-T1
Valid prediction for GeneMark_model.31618_t
Valid prediction for snap_scaffold_7-snap.2628-T1
Valid prediction for GlimmerHMM_glimmerT_18856-T1
Valid prediction for snap_scaffold_7-snap.2613-T1
Valid prediction for Augustus_model.g12756.t1
Valid prediction for GeneMark_model.31583_t
Valid prediction for GlimmerHMM_glimmerT_18867-T1
Valid prediction for snap_scaffold_7-snap.2614-T1
Valid prediction for GeneMark_model.31576_t
Valid prediction for GeneMark_model.31612_t
Valid prediction for Augustus_model.g12766.t1
Valid prediction for snap_scaffold_7-snap.2649-T1
Valid prediction for snap_scaffold_7-snap.2620-T1
Valid prediction for GeneMark_model.31588_t
Valid prediction for GlimmerHMM_glimmerT_18850-T1
Valid prediction for GeneMark_model.31570_t
Valid prediction for snap_scaffold_7-snap.2643-T1
Valid prediction for Augustus_model.g12768.t1
Valid prediction for GeneMark_model.31587_t
Couldn't classify 195496, 196845
Sorry, prediction pasa_asmbl_50146.p1 fails validation.
(CCT)	 TC	195496-196845	GC	CTG
Valid prediction for snap_scaffold_7-snap.2645-T1
Valid prediction for snap_scaffold_7-snap.2637-T1
Valid prediction for snap_scaffold_7-snap.2635-T1
Valid prediction for snap_scaffold_7-snap.2656-T1
Valid prediction for GeneMark_model.31617_t
Valid prediction for GlimmerHMM_glimmerT_18851-T1
Valid prediction for GeneMark_model.31571_t
Valid prediction for GlimmerHMM_glimmerT_18857-T1
Valid prediction for snap_scaffold_7-snap.2617-T1
Valid prediction for GeneMark_model.31610_t
Valid prediction for snap_scaffold_7-snap.2654-T1
Valid prediction for GeneMark_model.31590_t
Couldn't classify 195071, 195186
Sorry, prediction pasa_asmbl_50147.p1 fails validation.
(ATG)	 AT	191128-191818	GT	TTG
(ATG)	 AG	194484-194537	GC	AGG
(CAC)	 AG	195071-195186	GC	TGG
-recovered pasa_asmbl_50147.p1, initial, 191128, 191818
add_exon() Sorry, pasa_asmbl_50147.p1 194484-194537-initial-1 is invalid.
-recovered pasa_asmbl_50147.p1, initial, 194484, 194537
-recovered pasa_asmbl_50147.p1, internal, 194484, 194537
-recovered pasa_asmbl_50147.p1, internal, 195071, 195186
Valid prediction for GeneMark_model.31623_t
Valid prediction for GeneMark_model.31621_t
Valid prediction for GeneMark_model.31574_t
Valid prediction for GeneMark_model.31608_t
Valid prediction for GeneMark_model.31599_t
Valid prediction for Augustus_model.g12759.t1
Valid prediction for GeneMark_model.31569_t
Valid prediction for GlimmerHMM_glimmerT_18872-T1
Valid prediction for GeneMark_model.31592_t
Valid prediction for GeneMark_model.31581_t
Valid prediction for Augustus_model.g12767.t1
Couldn't classify 102224, 102317
Sorry, prediction pasa_asmbl_50151.p1 fails validation.
(ATG)	 AC	97809-97911	GT	AGG
(TTT)	 AG	98623-98687	GT	TGG
(GTG)	 AG	98852-98953	GT	AGG
(ACG)	 AG	100414-100528	GT	CGG
(GAG)	 AG	100620-100707	GT	AGG
(AAG)	 AG	102224-102317	GT	CGG
-recovered pasa_asmbl_50151.p1, initial, 97809, 97911
-recovered pasa_asmbl_50151.p1, internal, 98623, 98687
-recovered pasa_asmbl_50151.p1, internal, 98852, 98953
-recovered pasa_asmbl_50151.p1, internal, 100414, 100528
-recovered pasa_asmbl_50151.p1, internal, 100620, 100707
-recovered pasa_asmbl_50151.p1, internal, 102224, 102317
Valid prediction for Augustus_model.g12755.t1
Valid prediction for GlimmerHMM_glimmerT_18869-T1
Valid prediction for Augustus_model.g12763.t1
Valid prediction for GeneMark_model.31607_t
Valid prediction for GlimmerHMM_glimmerT_18859-T1
Valid prediction for snap_scaffold_7-snap.2646-T1
Valid prediction for GlimmerHMM_glimmerT_18863-T1
Valid prediction for snap_scaffold_7-snap.2612-T1
Valid prediction for GlimmerHMM_glimmerT_18864-T1
Valid prediction for snap_scaffold_7-snap.2616-T1
Valid prediction for snap_scaffold_7-snap.2650-T1
Valid prediction for Augustus_model.g12760.t1
Valid prediction for snap_scaffold_7-snap.2640-T1
Valid prediction for GeneMark_model.31614_t
Valid prediction for Augustus_model.g12769.t1
Valid prediction for GeneMark_model.31600_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18725, rend_intergenic: 15517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52456, rend_intergenic: 28335  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61125, rend_intergenic: 57918  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71416, rend_intergenic: 66501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109041, rend_intergenic: 103785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130127, rend_intergenic: 122942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133597, rend_intergenic: 131153  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152402, rend_intergenic: 146435  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157479, rend_intergenic: 155188  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163297, rend_intergenic: 157785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174956, rend_intergenic: 167594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180061, rend_intergenic: 178907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193646, rend_intergenic: 180122  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 199626
-exon list size: 725


building trellis

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81.7    
81.8    
82.0    
82.1    
82.3    
82.4    
82.5    
82.7    
82.8    
82.9    
83.1    
83.2    
83.4    
83.5    
83.6    
83.8    
83.9    
84.0    
84.2    
84.3    
84.5    
84.6    
84.7    
84.9    
85.0    
85.1    
85.3    
85.4    
85.6    
85.7    
85.8    
86.0    
86.1    
86.2    
86.4    
86.5    
86.7    
86.8    
86.9    
87.1    
87.2    
87.3    
87.5    
87.6    
87.8    
87.9    
88.0    
88.2    
88.3    
88.4    
88.6    
88.7    
88.9    
89.0    
89.1    
89.3    
89.4    
89.5    
89.7    
89.8    
90.0    
90.1    
90.2    
90.4    
90.5    
90.6    
90.8    
90.9    
91.1    
91.2    
91.3    
91.5    
91.6    
91.7    
91.9    
92.0    
92.2    
92.3    
92.4    
92.6    
92.7    
92.8    
93.0    
93.1    
93.3    
93.4    
93.5    
93.7    
93.8    
93.9    
94.1    
94.2    
94.4    
94.5    
94.6    
94.8    
94.9    
95.0    
95.2    
95.3    
95.5    
95.6    
95.7    
95.9    
96.0    
96.1    
96.3    
96.4    
96.6    
96.7    
96.8    
97.0    
97.1    
97.2    
97.4    
97.5    
97.7    
97.8    
97.9    
98.1    
98.2    
98.3    
98.5    
98.6    
98.8    
98.9    
99.0    
99.2    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 18725, rend_intergenic: 15517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52456, rend_intergenic: 28335  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61125, rend_intergenic: 57918  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71416, rend_intergenic: 66501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109041, rend_intergenic: 103785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130127, rend_intergenic: 122942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133597, rend_intergenic: 131153  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152402, rend_intergenic: 146435  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157479, rend_intergenic: 155188  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163297, rend_intergenic: 157785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174956, rend_intergenic: 167594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180061, rend_intergenic: 178907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193646, rend_intergenic: 180122  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 180556 - 199626
-exon list size: 58


building trellis

1.7    
3.3    
5.0    
6.7    
8.3    
10.0    
11.7    
13.3    
15.0    
16.7    
18.3    
20.0    
21.7    
23.3    
25.0    
26.7    
28.3    
30.0    
31.7    
33.3    
35.0    
36.7    
38.3    
40.0    
41.7    
43.3    
45.0    
46.7    
48.3    
50.0    
51.7    
53.3    
55.0    
56.7    
58.3    
60.0    
61.7    
63.3    
65.0    
66.7    
68.3    
70.0    
71.7    
73.3    
75.0    
76.7    
78.3    
80.0    
81.7    
83.3    
85.0    
86.7    
88.3    
90.0    
91.7    
93.3    
95.0    
96.7    
98.3    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 180695 - 199626
-exon list size: 56


building trellis

1.7    
3.4    
5.2    
6.9    
8.6    
10.3    
12.1    
13.8    
15.5    
17.2    
19.0    
20.7    
22.4    
24.1    
25.9    
27.6    
29.3    
31.0    
32.8    
34.5    
36.2    
37.9    
39.7    
41.4    
43.1    
44.8    
46.6    
48.3    
50.0    
51.7    
53.4    
55.2    
56.9    
58.6    
60.3    
62.1    
63.8    
65.5    
67.2    
69.0    
70.7    
72.4    
74.1    
75.9    
77.6    
79.3    
81.0    
82.8    
84.5    
86.2    
87.9    
89.7    
91.4    
93.1    
94.8    
96.6    
98.3    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 180695 - 193410
-exon list size: 46


building trellis

2.1    
4.2    
6.2    
8.3    
10.4    
12.5    
14.6    
16.7    
18.8    
20.8    
22.9    
25.0    
27.1    
29.2    
31.2    
33.3    
35.4    
37.5    
39.6    
41.7    
43.8    
45.8    
47.9    
50.0    
52.1    
54.2    
56.2    
58.3    
60.4    
62.5    
64.6    
66.7    
68.8    
70.8    
72.9    
75.0    
77.1    
79.2    
81.2    
83.3    
85.4    
87.5    
89.6    
91.7    
93.8    
95.8    
97.9    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support