-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_12532500-12754119

-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.2457-T1
Valid prediction for GeneMark_model.12625_t
Valid prediction for snap_scaffold_3-snap.2460-T1
Valid prediction for GeneMark_model.12634_t
Valid prediction for Augustus_model.g5014.t1
Valid prediction for GlimmerHMM_glimmerT_7642-T1
Valid prediction for GlimmerHMM_glimmerT_7645-T1
Valid prediction for Augustus_model.g5016.t1
Valid prediction for Augustus_model.g5011.t1
Valid prediction for Augustus_model.g5010.t1
Couldn't classify 119774, 120112
Sorry, prediction pasa_asmbl_40812.p1 fails validation.
(AGT)	 AC	119774-120112	GG	CAG
Valid prediction for GlimmerHMM_glimmerT_7649-T1
Valid prediction for GlimmerHMM_glimmerT_7628-T1
Valid prediction for GeneMark_model.12650_t
Valid prediction for GeneMark_model.12647_t
Couldn't classify 125872, 125908
Couldn't classify 126382, 126836
Sorry, prediction pasa_asmbl_40366.p2 fails validation.
(TTG)	 GG	125872-125908	GT	AGG
(GGA)	 AG	126382-126836	GG	CTG
Valid prediction for Augustus_model.g5024.t1
Valid prediction for GlimmerHMM_glimmerT_7638-T1
Valid prediction for snap_scaffold_3-snap.2458-T1
Valid prediction for GeneMark_model.12645_t
Valid prediction for GeneMark_model.12632_t
Valid prediction for GlimmerHMM_glimmerT_7633-T1
Valid prediction for CodingQuarry_transcript_46197-T1
Couldn't classify 130438, 130477
Sorry, prediction pasa_asmbl_40367.p1 fails validation.
(GAG)	 CA	130438-130477	GT	GGG
(AAC)	 AG	130554-131155	CC	AAC
-recovered pasa_asmbl_40367.p1, terminal, 130554, 131155
Valid prediction for GeneMark_model.12624_t
Valid prediction for GlimmerHMM_glimmerT_7637-T1
Valid prediction for GlimmerHMM_glimmerT_7635-T1
Valid prediction for Augustus_model.g5023.t1
Valid prediction for GlimmerHMM_glimmerT_7634-T1
Valid prediction for GlimmerHMM_glimmerT_7630-T1
Couldn't classify 42220, 42328
Sorry, prediction pasa_asmbl_40364.p1 fails validation.
(ACA)	 CC	42220-42328	GT	AGG
(GGA)	 AG	44735-45076	GT	CGG
(GCC)	 AG	46683-47935	TG	GAT
-recovered pasa_asmbl_40364.p1, terminal, 46683, 47935
-recovered pasa_asmbl_40364.p1, internal, 44735, 45076
Valid prediction for snap_scaffold_3-snap.2450-T1
Valid prediction for snap_scaffold_3-snap.2449-T1
Valid prediction for Augustus_model.g5017.t1
Valid prediction for GeneMark_model.12636_t
Valid prediction for GeneMark_model.12639_t
Valid prediction for snap_scaffold_3-snap.2455-T1
Valid prediction for snap_scaffold_3-snap.2468-T1
Valid prediction for GlimmerHMM_glimmerT_7643-T1
Valid prediction for Augustus_model.g5020.t1
Couldn't classify 39070, 39180
Sorry, prediction pasa_asmbl_40363.p1 fails validation.
(ATG)	 TA	38132-38205	GT	AGG
(TGC)	 AG	38448-38551	GT	CGG
(GTG)	 AG	38659-38828	GT	AGG
(GCC)	 AG	39070-39180	GG	CAG
-recovered pasa_asmbl_40363.p1, initial, 38132, 38205
-recovered pasa_asmbl_40363.p1, internal, 38448, 38551
-recovered pasa_asmbl_40363.p1, internal, 38659, 38828
Valid prediction for HiQ_model.g5009.t1
Valid prediction for GeneMark_model.12646_t
Valid prediction for Augustus_model.g5008.t1
Valid prediction for snap_scaffold_3-snap.2451-T1
Valid prediction for snap_scaffold_3-snap.2459-T1
Valid prediction for snap_scaffold_3-snap.2461-T1
Valid prediction for GeneMark_model.12651_t
Valid prediction for GeneMark_model.12642_t
Valid prediction for snap_scaffold_3-snap.2467-T1
Valid prediction for GeneMark_model.12631_t
Valid prediction for GeneMark_model.12635_t
Valid prediction for snap_scaffold_3-snap.2454-T1
Valid prediction for snap_scaffold_3-snap.2448-T1
Valid prediction for GlimmerHMM_glimmerT_7641-T1
Valid prediction for GlimmerHMM_glimmerT_7639-T1
Valid prediction for GeneMark_model.12620_t
Valid prediction for GlimmerHMM_glimmerT_7652-T1
Valid prediction for CodingQuarry_transcript_46198-T1
Valid prediction for GlimmerHMM_glimmerT_7648-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: -)Couldn't classify 5449, 5512
Couldn't classify 8086, 8573
Sorry, prediction pasa_asmbl_39635.p1 fails validation.
(GCA)	 CG	5449-5512	GC	GGG
(ATG)	 AG	8086-8573	GC	GCG
add_exon() Sorry, pasa_asmbl_39635.p1 8086-8573-initial-1 is invalid.
-recovered pasa_asmbl_39635.p1, initial, 8086, 8573
-recovered pasa_asmbl_39635.p1, internal, 8086, 8573
Valid prediction for GeneMark_model.12622_t
Valid prediction for Augustus_model.g5028.t1
Valid prediction for snap_scaffold_3-snap.2463-T1
Valid prediction for snap_scaffold_3-snap.2447-T1
Valid prediction for pasa_asmbl_39174.p1
Valid prediction for Augustus_model.g5019.t1
Valid prediction for pasa_asmbl_39169.p1
Valid prediction for CodingQuarry_transcript_46195-T1
Valid prediction for snap_scaffold_3-snap.2475-T1
Valid prediction for snap_scaffold_3-snap.2474-T1
Valid prediction for snap_scaffold_3-snap.2453-T1
Couldn't classify 45283, 45499
Sorry, prediction pasa_asmbl_39181.p1 fails validation.
(AGT)	 TC	45283-45499	GT	AGG
(ACA)	 AG	46785-46968	GT	AAG
(GGG)	 AG	47325-47516	GT	AAG
(CGT)	 AG	48121-48279	GT	TGG
(GTC)	 AG	48435-48593	GT	TGG
(GCA)	 AG	49026-49134	GT	AGG
(GCG)	 AG	49570-49679	GT	AGG
(ACA)	 AG	49808-49961	TT	GAT
-recovered pasa_asmbl_39181.p1, terminal, 49808, 49961
-recovered pasa_asmbl_39181.p1, internal, 46785, 46968
-recovered pasa_asmbl_39181.p1, internal, 47325, 47516
-recovered pasa_asmbl_39181.p1, internal, 48121, 48279
-recovered pasa_asmbl_39181.p1, internal, 48435, 48593
-recovered pasa_asmbl_39181.p1, internal, 49026, 49134
-recovered pasa_asmbl_39181.p1, internal, 49570, 49679
Valid prediction for GeneMark_model.12643_t
Valid prediction for CodingQuarry_transcript_46199-T1
Valid prediction for snap_scaffold_3-snap.2473-T1
Valid prediction for snap_scaffold_3-snap.2442-T1
Valid prediction for CodingQuarry_transcript_46196-T1
Valid prediction for Augustus_model.g5007.t1
Couldn't classify 79832, 80243
Couldn't classify 80522, 80685
Sorry, prediction pasa_asmbl_39178.p1 fails validation.
(AAG)	 AA	79832-80243	GT	GGG
(GAG)	 AG	80522-80685	GG	GGG
Valid prediction for Augustus_model.g5005.t1
Valid prediction for GeneMark_model.12652_t
Valid prediction for GlimmerHMM_glimmerT_7644-T1
Valid prediction for Augustus_model.g5006.t1
Valid prediction for GeneMark_model.12648_t
Valid prediction for snap_scaffold_3-snap.2465-T1
Valid prediction for snap_scaffold_3-snap.2472-T1
Valid prediction for HiQ_model.g5022.t1
Valid prediction for snap_scaffold_3-snap.2444-T1
Valid prediction for Augustus_model.g5025.t1
Valid prediction for GlimmerHMM_glimmerT_7646-T1
Valid prediction for GeneMark_model.12619_t
Valid prediction for Augustus_model.g5018.t1
Valid prediction for GlimmerHMM_glimmerT_7640-T1
Valid prediction for GlimmerHMM_glimmerT_7632-T1
Valid prediction for GlimmerHMM_glimmerT_7636-T1
Valid prediction for GeneMark_model.12621_t
Valid prediction for GeneMark_model.12649_t
Valid prediction for GeneMark_model.12628_t
Valid prediction for HiQ_model.g5021.t1
Valid prediction for Augustus_model.g5012.t1
Valid prediction for GlimmerHMM_glimmerT_7647-T1
Valid prediction for GeneMark_model.12627_t
Valid prediction for GeneMark_model.12638_t
Valid prediction for GeneMark_model.12633_t
Valid prediction for snap_scaffold_3-snap.2469-T1
Valid prediction for snap_scaffold_3-snap.2470-T1
Valid prediction for snap_scaffold_3-snap.2471-T1
Valid prediction for GeneMark_model.12629_t
Valid prediction for snap_scaffold_3-snap.2456-T1
Valid prediction for snap_scaffold_3-snap.2445-T1
Valid prediction for Augustus_model.g5015.t1
Valid prediction for pasa_asmbl_39718.p1
Valid prediction for snap_scaffold_3-snap.2452-T1
Valid prediction for Augustus_model.g5013.t1
Valid prediction for GeneMark_model.12640_t
Valid prediction for snap_scaffold_3-snap.2462-T1
Valid prediction for GlimmerHMM_glimmerT_7627-T1
Valid prediction for GlimmerHMM_glimmerT_7631-T1
Valid prediction for GeneMark_model.12641_t
Valid prediction for GeneMark_model.12644_t
Valid prediction for snap_scaffold_3-snap.2464-T1
Valid prediction for Augustus_model.g5003.t1
Valid prediction for snap_scaffold_3-snap.2466-T1
Valid prediction for Augustus_model.g5027.t1
Valid prediction for GlimmerHMM_glimmerT_7629-T1
Valid prediction for snap_scaffold_3-snap.2443-T1
Valid prediction for GlimmerHMM_glimmerT_7650-T1
Couldn't classify 62488, 62514
Couldn't classify 64260, 64289
Sorry, prediction pasa_asmbl_39725.p1 fails validation.
(ACG)	 GC	62488-62514	GT	TGG
(AGC)	 AG	63203-63328	GT	TGG
(ACT)	 AG	63913-63977	GT	GGG
(GAG)	 AG	64078-64141	GT	AGG
(ACT)	 AG	64260-64289	GG	TGG
-recovered pasa_asmbl_39725.p1, internal, 63203, 63328
-recovered pasa_asmbl_39725.p1, internal, 63913, 63977
-recovered pasa_asmbl_39725.p1, internal, 64078, 64141
Valid prediction for GeneMark_model.12637_t
Couldn't classify 123419, 123427
Sorry, prediction pasa_asmbl_39171.p1 fails validation.
(CTC)	 TG	123419-123427	GT	TGG
(GAC)	 AG	123656-123721	GT	AGG
(GCT)	 AG	123839-123979	GT	AGG
(CTG)	 AG	124738-124956	GT	ATG
(AAG)	 AG	125185-125255	GT	ATG
(GGA)	 AG	125361-125460	GT	AGG
(AAC)	 AG	125706-125888	GT	GGG
(GTG)	 AG	126250-126350	GT	TGG
(GCC)	 AG	126457-126553	GT	AGG
(GAC)	 AG	126653-126793	GA	GAG
-recovered pasa_asmbl_39171.p1, terminal, 126653, 126793
-recovered pasa_asmbl_39171.p1, internal, 123656, 123721
-recovered pasa_asmbl_39171.p1, internal, 123839, 123979
-recovered pasa_asmbl_39171.p1, internal, 124738, 124956
-recovered pasa_asmbl_39171.p1, internal, 125185, 125255
-recovered pasa_asmbl_39171.p1, internal, 125361, 125460
-recovered pasa_asmbl_39171.p1, internal, 125706, 125888
-recovered pasa_asmbl_39171.p1, internal, 126250, 126350
-recovered pasa_asmbl_39171.p1, internal, 126457, 126553
Valid prediction for HiQ_model.g5004.t1
Valid prediction for Augustus_model.g5026.t1
Valid prediction for snap_scaffold_3-snap.2446-T1
Valid prediction for GlimmerHMM_glimmerT_7651-T1

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

-building trellis in range 1 - 221620
-exon list size: 549


building trellis

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27.9    
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28.5    
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28.9    
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30.3    
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30.9    
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32.1    
32.3    
32.5    
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32.8    
33.0    
33.2    
33.4    
33.6    
33.8    
33.9    
34.1    
34.3    
34.5    
34.7    
34.8    
35.0    
35.2    
35.4    
35.6    
35.8    
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36.1    
36.3    
36.5    
36.7    
36.8    
37.0    
37.2    
37.4    
37.6    
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37.9    
38.1    
38.3    
38.5    
38.7    
38.8    
39.0    
39.2    
39.4    
39.6    
39.7    
39.9    
40.1    
40.3    
40.5    
40.7    
40.8    
41.0    
41.2    
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41.6    
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42.3    
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42.8    
43.0    
43.2    
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43.6    
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43.9    
44.1    
44.3    
44.5    
44.6    
44.8    
45.0    
45.2    
45.4    
45.6    
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48.1    
48.3    
48.5    
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48.8    
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49.2    
49.4    
49.5    
49.7    
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50.1    
50.3    
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50.6    
50.8    
51.0    
51.2    
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51.5    
51.7    
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52.1    
52.3    
52.5    
52.6    
52.8    
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53.2    
53.4    
53.5    
53.7    
53.9    
54.1    
54.3    
54.4    
54.6    
54.8    
55.0    
55.2    
55.4    
55.5    
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56.1    
56.3    
56.4    
56.6    
56.8    
57.0    
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58.1    
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58.4    
58.6    
58.8    
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60.3    
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60.6    
60.8    
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66.1    
66.2    
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66.6    
66.8    
67.0    
67.2    
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67.9    
68.1    
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68.6    
68.8    
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69.1    
69.3    
69.5    
69.7    
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70.2    
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70.8    
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71.3    
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72.8    
73.0    
73.1    
73.3    
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73.9    
74.0    
74.2    
74.4    
74.6    
74.8    
75.0    
75.1    
75.3    
75.5    
75.7    
75.9    
76.0    
76.2    
76.4    
76.6    
76.8    
77.0    
77.1    
77.3    
77.5    
77.7    
77.9    
78.0    
78.2    
78.4    
78.6    
78.8    
78.9    
79.1    
79.3    
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79.9    
80.0    
80.2    
80.4    
80.6    
80.8    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
82.0    
82.2    
82.4    
82.6    
82.8    
82.9    
83.1    
83.3    
83.5    
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83.8    
84.0    
84.2    
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84.6    
84.8    
84.9    
85.1    
85.3    
85.5    
85.7    
85.8    
86.0    
86.2    
86.4    
86.6    
86.8    
86.9    
87.1    
87.3    
87.5    
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87.8    
88.0    
88.2    
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88.6    
88.7    
88.9    
89.1    
89.3    
89.5    
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90.0    
90.2    
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90.7    
90.9    
91.1    
91.3    
91.5    
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91.8    
92.0    
92.2    
92.4    
92.6    
92.7    
92.9    
93.1    
93.3    
93.5    
93.6    
93.8    
94.0    
94.2    
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96.0    
96.2    
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97.6    
97.8    
98.0    
98.2    
98.4    
98.5    
98.7    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 35 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 31 predictions persist after filtering for low support