-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_13739849-13947684

-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_3-snap.2665-T1
Valid prediction for Augustus_model.g5169.t1
Valid prediction for snap_scaffold_3-snap.2667-T1
Valid prediction for GlimmerHMM_glimmerT_7811-T1
Valid prediction for snap_scaffold_3-snap.2660-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.2662-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.2655-T1
Valid prediction for Augustus_model.g5159.t1
Valid prediction for snap_scaffold_3-snap.2661-T1
Valid prediction for GeneMark_model.12825_t
Valid prediction for HiQ_model.g5173.t1
Valid prediction for snap_scaffold_3-snap.2669-T1
Couldn't classify 163094, 163426
Sorry, prediction pasa_asmbl_40429.p1 fails validation.
(TGC)	 GT	163094-163426	GT	TGG
(CAA)	 AG	164306-164686	AC	GAA
-recovered pasa_asmbl_40429.p1, terminal, 164306, 164686
Valid prediction for GlimmerHMM_glimmerT_7834-T1
Valid prediction for GlimmerHMM_glimmerT_7824-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_7833-T1
Valid prediction for GlimmerHMM_glimmerT_7825-T1
Valid prediction for GlimmerHMM_glimmerT_7820-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_7836-T1
Valid prediction for GeneMark_model.12816_t
Valid prediction for Augustus_model.g5167.t1
Valid prediction for GlimmerHMM_glimmerT_7805-T1
Valid prediction for Augustus_model.g5153.t1
Valid prediction for Augustus_model.g5176.t1
Valid prediction for snap_scaffold_3-snap.2654-T1
Valid prediction for Augustus_model.g5149.t1
Valid prediction for HiQ_model.g5172.t1
Valid prediction for snap_scaffold_3-snap.2659-T1
Valid prediction for snap_scaffold_3-snap.2672-T1
Couldn't classify 28320, 28473
Sorry, prediction pasa_asmbl_40416.p1 fails validation.
(AGT)	 TC	28320-28473	GT	AGG
(ATC)	 AG	29079-29206	GT	AGG
(GTC)	 AG	29306-29467	TA	AGT
-recovered pasa_asmbl_40416.p1, terminal, 29306, 29467
-recovered pasa_asmbl_40416.p1, internal, 29079, 29206
Valid prediction for snap_scaffold_3-snap.2663-T1
Valid prediction for CodingQuarry_transcript_46230-T1
Couldn't classify 149752, 150171
Sorry, prediction pasa_asmbl_39690.p1 fails validation.
(GGT)	 TG	149752-150171	CA	CAC
Valid prediction for GlimmerHMM_glimmerT_7808-T1
Valid prediction for GlimmerHMM_glimmerT_7806-T1
Valid prediction for snap_scaffold_3-snap.2649-T1
Valid prediction for GeneMark_model.12808_t
Valid prediction for GeneMark_model.12822_t
Valid prediction for snap_scaffold_3-snap.2653-T1
Valid prediction for snap_scaffold_3-snap.2671-T1
Valid prediction for GlimmerHMM_glimmerT_7842-T1
Valid prediction for Augustus_model.g5170.t1
Valid prediction for pasa_asmbl_40424.p1
Valid prediction for pasa_asmbl_40419.p1
Valid prediction for GlimmerHMM_glimmerT_7831-T1
Valid prediction for snap_scaffold_3-snap.2645-T1
Valid prediction for snap_scaffold_3-snap.2680-T1
Valid prediction for GlimmerHMM_glimmerT_7830-T1
Valid prediction for GlimmerHMM_glimmerT_7829-T1
Valid prediction for GeneMark_model.12821_t
Valid prediction for GlimmerHMM_glimmerT_7813-T1
Valid prediction for Augustus_model.g5174.t1
Valid prediction for CodingQuarry_transcript_46232-T1
Valid prediction for snap_scaffold_3-snap.2646-T1
Valid prediction for snap_scaffold_3-snap.2673-T1
Valid prediction for Augustus_model.g5155.t1
Valid prediction for snap_scaffold_3-snap.2668-T1
Valid prediction for GlimmerHMM_glimmerT_7817-T1
Valid prediction for GlimmerHMM_glimmerT_7809-T1
Valid prediction for GlimmerHMM_glimmerT_7841-T1
Valid prediction for CodingQuarry_transcript_46231-T1
Valid prediction for GeneMark_model.12819_t
Valid prediction for GeneMark_model.12818_t
Valid prediction for Augustus_model.g5177.t1
Valid prediction for GeneMark_model.12827_t
Valid prediction for HiQ_model.g5162.t1
Valid prediction for GeneMark_model.12803_t
Valid prediction for GlimmerHMM_glimmerT_7827-T1
Valid prediction for GlimmerHMM_glimmerT_7832-T1
Valid prediction for snap_scaffold_3-snap.2670-T1
Valid prediction for snap_scaffold_3-snap.2677-T1
Valid prediction for CodingQuarry_transcript_46233-T1
Valid prediction for GeneMark_model.12824_t
Valid prediction for Augustus_model.g5171.t1
Valid prediction for GlimmerHMM_glimmerT_7821-T1
Valid prediction for GeneMark_model.12805_t
Valid prediction for snap_scaffold_3-snap.2651-T1
Valid prediction for Augustus_model.g5151.t1
Valid prediction for snap_scaffold_3-snap.2674-T1
Valid prediction for GeneMark_model.12823_t
Valid prediction for GeneMark_model.12826_t
Valid prediction for Augustus_model.g5163.t1
Valid prediction for snap_scaffold_3-snap.2675-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 snap_scaffold_3-snap.2658-T1
Valid prediction for GlimmerHMM_glimmerT_7839-T1
Valid prediction for Augustus_model.g5150.t1
Valid prediction for GeneMark_model.12810_t
Valid prediction for Augustus_model.g5168.t1
Valid prediction for snap_scaffold_3-snap.2678-T1
Valid prediction for GlimmerHMM_glimmerT_7840-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_7816-T1
Valid prediction for GeneMark_model.12811_t
Valid prediction for GlimmerHMM_glimmerT_7835-T1
Valid prediction for GlimmerHMM_glimmerT_7819-T1
Valid prediction for GeneMark_model.12804_t
Valid prediction for GlimmerHMM_glimmerT_7807-T1
Valid prediction for HiQ_model.g5160.t1
Valid prediction for snap_scaffold_3-snap.2657-T1
Valid prediction for snap_scaffold_3-snap.2679-T1
Couldn't classify 172903, 173038
Sorry, prediction pasa_asmbl_39249.p1 fails validation.
(AAT)	 AG	172903-173038	GT	GGG
(GTC)	 AG	173595-173647	GT	AAG
(GAG)	 AG	173760-173854	GT	AAG
(TTA)	 AG	174175-174311	GT	TGG
(GGG)	 AG	174406-174597	GC	AGG
(TCT)	 AG	174694-174739	GT	GAG
(TAC)	 AG	175025-175115	GT	TTG
(ATG)	 AG	175546-175569	CA	AAC
-recovered pasa_asmbl_39249.p1, terminal, 175546, 175569
-recovered pasa_asmbl_39249.p1, internal, 172903, 173038
-recovered pasa_asmbl_39249.p1, internal, 173595, 173647
-recovered pasa_asmbl_39249.p1, internal, 173760, 173854
-recovered pasa_asmbl_39249.p1, internal, 174175, 174311
-recovered pasa_asmbl_39249.p1, internal, 174406, 174597
-recovered pasa_asmbl_39249.p1, internal, 174694, 174739
-recovered pasa_asmbl_39249.p1, internal, 175025, 175115
Valid prediction for Augustus_model.g5165.t1
Valid prediction for Augustus_model.g5164.t1
Valid prediction for snap_scaffold_3-snap.2647-T1
Valid prediction for Augustus_model.g5158.t1
Valid prediction for Augustus_model.g5152.t1
Valid prediction for GlimmerHMM_glimmerT_7828-T1
Valid prediction for snap_scaffold_3-snap.2656-T1
Valid prediction for GlimmerHMM_glimmerT_7810-T1
Valid prediction for GlimmerHMM_glimmerT_7814-T1
Valid prediction for snap_scaffold_3-snap.2676-T1
Valid prediction for GlimmerHMM_glimmerT_7838-T1
Valid prediction for GeneMark_model.12814_t
Valid prediction for Augustus_model.g5157.t1
Valid prediction for GlimmerHMM_glimmerT_7822-T1
Valid prediction for GeneMark_model.12806_t
Valid prediction for snap_scaffold_3-snap.2650-T1
Valid prediction for snap_scaffold_3-snap.2648-T1
Valid prediction for GlimmerHMM_glimmerT_7815-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.12809_t
Valid prediction for CodingQuarry_transcript_46228-T1
Valid prediction for snap_scaffold_3-snap.2652-T1
Valid prediction for HiQ_model.g5166.t1
Couldn't classify 146281, 146438
Couldn't classify 151000, 151083
Sorry, prediction pasa_asmbl_39252.p1 fails validation.
(TTT)	 GG	146281-146438	GT	AGG
(CTC)	 AG	146664-146756	GT	AGG
(ACT)	 AG	147516-147575	GT	AAG
(GGA)	 AG	148079-148099	GT	TTG
(AAA)	 AG	148873-148966	GT	TGG
(CAG)	 AG	149271-149315	GT	AGG
(GGT)	 AG	151000-151083	GT	AAG
add_exon() Sorry, pasa_asmbl_39252.p1 147516-147575-terminal-1 is invalid.
-recovered pasa_asmbl_39252.p1, terminal, 147516, 147575
-recovered pasa_asmbl_39252.p1, internal, 146664, 146756
-recovered pasa_asmbl_39252.p1, internal, 147516, 147575
-recovered pasa_asmbl_39252.p1, internal, 148079, 148099
-recovered pasa_asmbl_39252.p1, internal, 148873, 148966
-recovered pasa_asmbl_39252.p1, internal, 149271, 149315
-recovered pasa_asmbl_39252.p1, internal, 151000, 151083
Valid prediction for Augustus_model.g5154.t1
Valid prediction for GeneMark_model.12812_t
Valid prediction for Augustus_model.g5161.t1
Valid prediction for Augustus_model.g5156.t1
Valid prediction for GlimmerHMM_glimmerT_7812-T1
Valid prediction for snap_scaffold_3-snap.2666-T1
Valid prediction for GeneMark_model.12813_t
Valid prediction for GlimmerHMM_glimmerT_7818-T1
Valid prediction for GlimmerHMM_glimmerT_7823-T1
Valid prediction for GlimmerHMM_glimmerT_7837-T1
Valid prediction for snap_scaffold_3-snap.2664-T1
Couldn't classify 120946, 121080
Couldn't classify 122268, 122360
Sorry, prediction pasa_asmbl_39697.p1 fails validation.
(GAC)	 GG	120946-121080	GT	AGG
(GGG)	 AG	122027-122125	GT	AGG
(GGT)	 AG	122268-122360	GT	AGG
-recovered pasa_asmbl_39697.p1, internal, 122027, 122125
-recovered pasa_asmbl_39697.p1, internal, 122268, 122360
Valid prediction for Augustus_model.g5175.t1
Valid prediction for GlimmerHMM_glimmerT_7826-T1

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

-building trellis in range 1 - 207836
-exon list size: 404


building trellis

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24.9    
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27.1    
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27.6    
27.8    
28.1    
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28.6    
28.8    
29.1    
29.3    
29.6    
29.8    
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30.3    
30.5    
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31.5    
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32.0    
32.3    
32.5    
32.8    
33.0    
33.3    
33.5    
33.7    
34.0    
34.2    
34.5    
34.7    
35.0    
35.2    
35.5    
35.7    
36.0    
36.2    
36.5    
36.7    
36.9    
37.2    
37.4    
37.7    
37.9    
38.2    
38.4    
38.7    
38.9    
39.2    
39.4    
39.7    
39.9    
40.1    
40.4    
40.6    
40.9    
41.1    
41.4    
41.6    
41.9    
42.1    
42.4    
42.6    
42.9    
43.1    
43.3    
43.6    
43.8    
44.1    
44.3    
44.6    
44.8    
45.1    
45.3    
45.6    
45.8    
46.1    
46.3    
46.6    
46.8    
47.0    
47.3    
47.5    
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48.0    
48.3    
48.5    
48.8    
49.0    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
51.0    
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51.5    
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52.0    
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53.2    
53.4    
53.7    
53.9    
54.2    
54.4    
54.7    
54.9    
55.2    
55.4    
55.7    
55.9    
56.2    
56.4    
56.7    
56.9    
57.1    
57.4    
57.6    
57.9    
58.1    
58.4    
58.6    
58.9    
59.1    
59.4    
59.6    
59.9    
60.1    
60.3    
60.6    
60.8    
61.1    
61.3    
61.6    
61.8    
62.1    
62.3    
62.6    
62.8    
63.1    
63.3    
63.5    
63.8    
64.0    
64.3    
64.5    
64.8    
65.0    
65.3    
65.5    
65.8    
66.0    
66.3    
66.5    
66.7    
67.0    
67.2    
67.5    
67.7    
68.0    
68.2    
68.5    
68.7    
69.0    
69.2    
69.5    
69.7    
70.0    
70.2    
70.4    
70.7    
70.9    
71.2    
71.4    
71.7    
71.9    
72.2    
72.4    
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72.9    
73.2    
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73.6    
73.9    
74.1    
74.4    
74.6    
74.9    
75.1    
75.4    
75.6    
75.9    
76.1    
76.4    
76.6    
76.8    
77.1    
77.3    
77.6    
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78.1    
78.3    
78.6    
78.8    
79.1    
79.3    
79.6    
79.8    
80.0    
80.3    
80.5    
80.8    
81.0    
81.3    
81.5    
81.8    
82.0    
82.3    
82.5    
82.8    
83.0    
83.3    
83.5    
83.7    
84.0    
84.2    
84.5    
84.7    
85.0    
85.2    
85.5    
85.7    
86.0    
86.2    
86.5    
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86.9    
87.2    
87.4    
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87.9    
88.2    
88.4    
88.7    
88.9    
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89.9    
90.1    
90.4    
90.6    
90.9    
91.1    
91.4    
91.6    
91.9    
92.1    
92.4    
92.6    
92.9    
93.1    
93.3    
93.6    
93.8    
94.1    
94.3    
94.6    
94.8    
95.1    
95.3    
95.6    
95.8    
96.1    
96.3    
96.6    
96.8    
97.0    
97.3    
97.5    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 37 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 34 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 195346 - 207836
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal

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