-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_13916056-14083914

-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: +)Couldn't classify 77151, 77274
Sorry, prediction pasa_asmbl_40477.p1 fails validation.
(ATG)	 AG	73050-73094	GT	AGG
(TGT)	 AG	73519-73621	GT	AAG
(AAA)	 AG	74616-75440	GT	GGG
(CTC)	 AG	77011-77074	GT	CAG
(GGC)	 AG	77151-77274	GG	CAG
-recovered pasa_asmbl_40477.p1, initial, 73050, 73094
-recovered pasa_asmbl_40477.p1, internal, 73050, 73094
-recovered pasa_asmbl_40477.p1, internal, 73519, 73621
-recovered pasa_asmbl_40477.p1, internal, 74616, 75440
-recovered pasa_asmbl_40477.p1, internal, 77011, 77074
Valid prediction for snap_scaffold_3-snap.2675-T1
Valid prediction for GlimmerHMM_glimmerT_7680-T1
Valid prediction for snap_scaffold_3-snap.2677-T1
Valid prediction for CodingQuarry_transcript_46338-T1
Valid prediction for GlimmerHMM_glimmerT_7682-T1
Valid prediction for snap_scaffold_3-snap.2685-T1
Valid prediction for snap_scaffold_3-snap.2669-T1
Valid prediction for GlimmerHMM_glimmerT_7674-T1
Couldn't classify 90053, 90094
Sorry, prediction pasa_asmbl_40488.p1 fails validation.
(GCG)	 TG	90053-90094	GT	AGG
(TGT)	 AG	90842-90938	GT	GGG
(TTA)	 AG	93908-95452	GT	GGG
(AAG)	 AG	97614-97783	GA	GAG
-recovered pasa_asmbl_40488.p1, terminal, 97614, 97783
-recovered pasa_asmbl_40488.p1, internal, 90842, 90938
-recovered pasa_asmbl_40488.p1, internal, 93908, 95452
Valid prediction for snap_scaffold_3-snap.2674-T1
Valid prediction for Augustus_model.g5034.t1
Valid prediction for snap_scaffold_3-snap.2692-T1
Valid prediction for Augustus_model.g5045.t1
Valid prediction for Augustus_model.g5047.t1
Valid prediction for Augustus_model.g5041.t1
Valid prediction for snap_scaffold_3-snap.2661-T1
Valid prediction for Augustus_model.g5055.t1
Valid prediction for Augustus_model.g5040.t1
Valid prediction for Augustus_model.g5052.t1
Valid prediction for GlimmerHMM_glimmerT_7679-T1
Valid prediction for snap_scaffold_3-snap.2680-T1
Valid prediction for GlimmerHMM_glimmerT_7665-T1
Couldn't classify 103731, 103802
Sorry, prediction pasa_asmbl_40494.p1 fails validation.
(ATG)	 TG	98272-98343	GT	AGG
(ATG)	 AG	100562-100689	GT	CGG
(CCA)	 AG	100869-101040	GT	TGG
(ATG)	 AG	103068-103268	GT	AGG
(ACC)	 AG	103731-103802	AA	GCA
-recovered pasa_asmbl_40494.p1, initial, 98272, 98343
-recovered pasa_asmbl_40494.p1, initial, 100562, 100689
-recovered pasa_asmbl_40494.p1, initial, 103068, 103268
-recovered pasa_asmbl_40494.p1, internal, 100562, 100689
-recovered pasa_asmbl_40494.p1, internal, 100869, 101040
-recovered pasa_asmbl_40494.p1, internal, 103068, 103268
Valid prediction for GlimmerHMM_glimmerT_7684-T1
Valid prediction for Augustus_model.g5053.t1
Valid prediction for Augustus_model.g5029.t1
Valid prediction for snap_scaffold_3-snap.2664-T1
Valid prediction for Augustus_model.g5031.t1
Valid prediction for snap_scaffold_3-snap.2668-T1
Valid prediction for snap_scaffold_3-snap.2662-T1
Valid prediction for GlimmerHMM_glimmerT_7668-T1
Valid prediction for snap_scaffold_3-snap.2690-T1
Valid prediction for GlimmerHMM_glimmerT_7672-T1
Valid prediction for HiQ_model.g5042.t1
Valid prediction for GlimmerHMM_glimmerT_7664-T1
Valid prediction for Augustus_model.g5044.t1
Valid prediction for Augustus_model.g5048.t1
Valid prediction for CodingQuarry_transcript_46339-T1
Valid prediction for Augustus_model.g5054.t1
Valid prediction for GlimmerHMM_glimmerT_7685-T1
Valid prediction for Augustus_model.g5043.t1
Valid prediction for GlimmerHMM_glimmerT_7676-T1
Valid prediction for GlimmerHMM_glimmerT_7687-T1
Valid prediction for snap_scaffold_3-snap.2683-T1
Couldn't classify 153162, 153476
Sorry, prediction pasa_asmbl_40500.p1 fails validation.
(ATG)	 AG	153162-153476	AA	ACA
Valid prediction for Augustus_model.g5038.t1
Valid prediction for Augustus_model.g5056.t1
Valid prediction for snap_scaffold_3-snap.2678-T1
Valid prediction for Augustus_model.g5032.t1
Valid prediction for snap_scaffold_3-snap.2673-T1
Valid prediction for GlimmerHMM_glimmerT_7678-T1
Valid prediction for GlimmerHMM_glimmerT_7691-T1
Valid prediction for GlimmerHMM_glimmerT_7689-T1
Valid prediction for snap_scaffold_3-snap.2667-T1
Valid prediction for snap_scaffold_3-snap.2691-T1
Valid prediction for GlimmerHMM_glimmerT_7688-T1
Valid prediction for GlimmerHMM_glimmerT_7670-T1
Valid prediction for snap_scaffold_3-snap.2693-T1
Valid prediction for GlimmerHMM_glimmerT_7669-T1
Valid prediction for snap_scaffold_3-snap.2689-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 97741, 97854
Sorry, prediction pasa_asmbl_39317.p1 fails validation.
(ATG)	 CT	96786-96868	GT	AGG
(AGA)	 AG	97009-97077	GT	GGG
(GCA)	 AG	97288-97434	GT	AGG
(GTG)	 AG	97510-97666	GT	TGG
(ACA)	 AG	97741-97854	TA	AGT
-recovered pasa_asmbl_39317.p1, initial, 96786, 96868
-recovered pasa_asmbl_39317.p1, internal, 97009, 97077
-recovered pasa_asmbl_39317.p1, internal, 97288, 97434
-recovered pasa_asmbl_39317.p1, internal, 97510, 97666
Valid prediction for GlimmerHMM_glimmerT_7675-T1
Valid prediction for Augustus_model.g5046.t1
Valid prediction for snap_scaffold_3-snap.2684-T1
Valid prediction for snap_scaffold_3-snap.2672-T1
Valid prediction for GlimmerHMM_glimmerT_7666-T1
Valid prediction for GlimmerHMM_glimmerT_7683-T1
Valid prediction for snap_scaffold_3-snap.2671-T1
Valid prediction for GlimmerHMM_glimmerT_7690-T1
Valid prediction for GlimmerHMM_glimmerT_7677-T1
Valid prediction for Augustus_model.g5050.t1
Valid prediction for GlimmerHMM_glimmerT_7686-T1
Valid prediction for GlimmerHMM_glimmerT_7667-T1
Valid prediction for snap_scaffold_3-snap.2686-T1
Valid prediction for snap_scaffold_3-snap.2694-T1
Valid prediction for Augustus_model.g5033.t1
Valid prediction for snap_scaffold_3-snap.2687-T1
Valid prediction for snap_scaffold_3-snap.2665-T1
Valid prediction for GlimmerHMM_glimmerT_7681-T1
Valid prediction for Augustus_model.g5030.t1
Valid prediction for Augustus_model.g5036.t1
Valid prediction for HiQ_model.g5039.t1
Valid prediction for snap_scaffold_3-snap.2666-T1
Valid prediction for Augustus_model.g5049.t1
Valid prediction for snap_scaffold_3-snap.2682-T1
Valid prediction for Augustus_model.g5037.t1
Valid prediction for snap_scaffold_3-snap.2688-T1
Valid prediction for Augustus_model.g5051.t1
Valid prediction for snap_scaffold_3-snap.2681-T1
Valid prediction for snap_scaffold_3-snap.2676-T1
Couldn't classify 120134, 120193
Sorry, prediction pasa_asmbl_39315.p1 fails validation.
(TTT)	 GG	120134-120193	GT	GGG
(GAT)	 AG	120335-120436	GT	AGG
(AGA)	 AG	120594-120658	GT	AGG
(AGT)	 AG	121252-121438	GT	AGG
(GCC)	 AG	122229-122288	AA	AAA
-recovered pasa_asmbl_39315.p1, terminal, 122229, 122288
-recovered pasa_asmbl_39315.p1, internal, 120335, 120436
-recovered pasa_asmbl_39315.p1, internal, 120594, 120658
-recovered pasa_asmbl_39315.p1, internal, 121252, 121438
Valid prediction for GlimmerHMM_glimmerT_7671-T1
Valid prediction for GlimmerHMM_glimmerT_7673-T1
Valid prediction for Augustus_model.g5035.t1
Valid prediction for snap_scaffold_3-snap.2663-T1
Valid prediction for snap_scaffold_3-snap.2670-T1
Valid prediction for snap_scaffold_3-snap.2679-T1

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

-building trellis in range 1 - 167859
-exon list size: 255


building trellis

0.4    
0.8    
1.2    
1.6    
1.9    
2.3    
2.7    
3.1    
3.5    
3.9    
4.3    
4.7    
5.1    
5.4    
5.8    
6.2    
6.6    
7.0    
7.4    
7.8    
8.2    
8.6    
8.9    
9.3    
9.7    
10.1    
10.5    
10.9    
11.3    
11.7    
12.1    
12.5    
12.8    
13.2    
13.6    
14.0    
14.4    
14.8    
15.2    
15.6    
16.0    
16.3    
16.7    
17.1    
17.5    
17.9    
18.3    
18.7    
19.1    
19.5    
19.8    
20.2    
20.6    
21.0    
21.4    
21.8    
22.2    
22.6    
23.0    
23.3    
23.7    
24.1    
24.5    
24.9    
25.3    
25.7    
26.1    
26.5    
26.8    
27.2    
27.6    
28.0    
28.4    
28.8    
29.2    
29.6    
30.0    
30.4    
30.7    
31.1    
31.5    
31.9    
32.3    
32.7    
33.1    
33.5    
33.9    
34.2    
34.6    
35.0    
35.4    
35.8    
36.2    
36.6    
37.0    
37.4    
37.7    
38.1    
38.5    
38.9    
39.3    
39.7    
40.1    
40.5    
40.9    
41.2    
41.6    
42.0    
42.4    
42.8    
43.2    
43.6    
44.0    
44.4    
44.7    
45.1    
45.5    
45.9    
46.3    
46.7    
47.1    
47.5    
47.9    
48.2    
48.6    
49.0    
49.4    
49.8    
50.2    
50.6    
51.0    
51.4    
51.8    
52.1    
52.5    
52.9    
53.3    
53.7    
54.1    
54.5    
54.9    
55.3    
55.6    
56.0    
56.4    
56.8    
57.2    
57.6    
58.0    
58.4    
58.8    
59.1    
59.5    
59.9    
60.3    
60.7    
61.1    
61.5    
61.9    
62.3    
62.6    
63.0    
63.4    
63.8    
64.2    
64.6    
65.0    
65.4    
65.8    
66.1    
66.5    
66.9    
67.3    
67.7    
68.1    
68.5    
68.9    
69.3    
69.6    
70.0    
70.4    
70.8    
71.2    
71.6    
72.0    
72.4    
72.8    
73.2    
73.5    
73.9    
74.3    
74.7    
75.1    
75.5    
75.9    
76.3    
76.7    
77.0    
77.4    
77.8    
78.2    
78.6    
79.0    
79.4    
79.8    
80.2    
80.5    
80.9    
81.3    
81.7    
82.1    
82.5    
82.9    
83.3    
83.7    
84.0    
84.4    
84.8    
85.2    
85.6    
86.0    
86.4    
86.8    
87.2    
87.5    
87.9    
88.3    
88.7    
89.1    
89.5    
89.9    
90.3    
90.7    
91.1    
91.4    
91.8    
92.2    
92.6    
93.0    
93.4    
93.8    
94.2    
94.6    
94.9    
95.3    
95.7    
96.1    
96.5    
96.9    
97.3    
97.7    
98.1    
98.4    
98.8    
99.2    
99.6    
-found 32 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support