-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_6924996-7157317

-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_2-snap.1516-T1
Valid prediction for Augustus_model.g2701.t1
Valid prediction for GlimmerHMM_glimmerT_4016-T1
Valid prediction for snap_scaffold_2-snap.1527-T1
Couldn't classify 206234, 206381
Couldn't classify 210797, 210982
Sorry, prediction pasa_asmbl_24531.p1 fails validation.
(AGG)	 CA	206234-206381	GT	ACG
(ATT)	 AG	206641-206891	GT	GGG
(GAG)	 AG	207939-208361	GT	AGG
(GAC)	 AG	208592-208702	GT	AGG
(TAC)	 AG	208903-209099	GT	AGG
(TGA)	 AG	209262-209756	GT	AGG
(GTT)	 AG	210405-210522	GT	AGG
(GTT)	 AG	210797-210982	GT	AGG
-recovered pasa_asmbl_24531.p1, internal, 206641, 206891
-recovered pasa_asmbl_24531.p1, internal, 207939, 208361
-recovered pasa_asmbl_24531.p1, internal, 208592, 208702
-recovered pasa_asmbl_24531.p1, internal, 208903, 209099
-recovered pasa_asmbl_24531.p1, internal, 209262, 209756
-recovered pasa_asmbl_24531.p1, internal, 210405, 210522
-recovered pasa_asmbl_24531.p1, internal, 210797, 210982
Valid prediction for snap_scaffold_2-snap.1510-T1
Valid prediction for Augustus_model.g2691.t1
Valid prediction for Augustus_model.g2683.t1
Valid prediction for snap_scaffold_2-snap.1495-T1
Valid prediction for GlimmerHMM_glimmerT_4005-T1
Valid prediction for GlimmerHMM_glimmerT_4028-T1
Valid prediction for snap_scaffold_2-snap.1494-T1
Valid prediction for snap_scaffold_2-snap.1513-T1
Valid prediction for GlimmerHMM_glimmerT_4035-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.1525-T1
Valid prediction for Augustus_model.g2704.t1
Valid prediction for GlimmerHMM_glimmerT_4006-T1
Couldn't classify 193350, 193751
Couldn't classify 194261, 194392
Sorry, prediction pasa_asmbl_24527.p1 fails validation.
(AAG)	 CT	193350-193751	GT	AGG
(GCC)	 AG	194261-194392	CT	GCC
Valid prediction for GlimmerHMM_glimmerT_4026-T1
Valid prediction for Augustus_model.g2711.t1
Valid prediction for snap_scaffold_2-snap.1505-T1
Valid prediction for snap_scaffold_2-snap.1521-T1
Valid prediction for Augustus_model.g2696.t1
Valid prediction for snap_scaffold_2-snap.1492-T1
Valid prediction for Augustus_model.g2703.t1
Valid prediction for snap_scaffold_2-snap.1530-T1
Valid prediction for GlimmerHMM_glimmerT_4024-T1
Couldn't classify 206234, 206381
Sorry, prediction pasa_asmbl_24529.p1 fails validation.
(AGG)	 CA	206234-206381	GT	ACG
(ATT)	 AG	206641-206912	GC	AAG
-recovered pasa_asmbl_24529.p1, terminal, 206641, 206912
-recovered pasa_asmbl_24529.p1, internal, 206641, 206912
Valid prediction for GlimmerHMM_glimmerT_4023-T1
Valid prediction for snap_scaffold_2-snap.1526-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for Augustus_model.g2694.t1
Valid prediction for snap_scaffold_2-snap.1514-T1
Valid prediction for snap_scaffold_2-snap.1529-T1
Valid prediction for snap_scaffold_2-snap.1520-T1
Valid prediction for GlimmerHMM_glimmerT_4031-T1
Valid prediction for Augustus_model.g2698.t1
Valid prediction for snap_scaffold_2-snap.1524-T1
Valid prediction for GlimmerHMM_glimmerT_4032-T1
Valid prediction for Augustus_model.g2697.t1
Valid prediction for GlimmerHMM_glimmerT_4025-T1
Valid prediction for Augustus_model.g2707.t1
Valid prediction for snap_scaffold_2-snap.1515-T1
Valid prediction for GlimmerHMM_glimmerT_4013-T1
Valid prediction for snap_scaffold_2-snap.1517-T1
Valid prediction for GlimmerHMM_glimmerT_4038-T1
Valid prediction for snap_scaffold_2-snap.1518-T1
Valid prediction for GlimmerHMM_glimmerT_4018-T1
Valid prediction for Augustus_model.g2700.t1
Valid prediction for Augustus_model.g2710.t1
Valid prediction for GlimmerHMM_glimmerT_4027-T1
Valid prediction for snap_scaffold_2-snap.1508-T1
Valid prediction for GlimmerHMM_glimmerT_4037-T1
Valid prediction for Augustus_model.g2682.t1
Valid prediction for GlimmerHMM_glimmerT_4019-T1
Valid prediction for Augustus_model.g2684.t1
Valid prediction for HiQ_model.g2713.t1
Valid prediction for Augustus_model.g2702.t1
Valid prediction for snap_scaffold_2-snap.1511-T1
Valid prediction for GlimmerHMM_glimmerT_4012-T1
Valid prediction for GlimmerHMM_glimmerT_4034-T1
Valid prediction for snap_scaffold_2-snap.1496-T1
Valid prediction for snap_scaffold_2-snap.1528-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 Augustus_model.g2688.t1
Valid prediction for Augustus_model.g2685.t1
Valid prediction for GlimmerHMM_glimmerT_4021-T1
Valid prediction for snap_scaffold_2-snap.1519-T1
Valid prediction for snap_scaffold_2-snap.1504-T1
Valid prediction for Augustus_model.g2699.t1
Valid prediction for snap_scaffold_2-snap.1501-T1
Valid prediction for snap_scaffold_2-snap.1523-T1
Valid prediction for snap_scaffold_2-snap.1503-T1
Valid prediction for snap_scaffold_2-snap.1512-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_4029-T1
Valid prediction for snap_scaffold_2-snap.1500-T1
Valid prediction for snap_scaffold_2-snap.1493-T1
Valid prediction for snap_scaffold_2-snap.1509-T1
Valid prediction for Augustus_model.g2693.t1
Valid prediction for GlimmerHMM_glimmerT_4004-T1
Valid prediction for Augustus_model.g2695.t1
Valid prediction for Augustus_model.g2706.t1
Valid prediction for snap_scaffold_2-snap.1497-T1
Valid prediction for snap_scaffold_2-snap.1507-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g2709.t1
Valid prediction for Augustus_model.g2692.t1
Valid prediction for snap_scaffold_2-snap.1499-T1
Valid prediction for Augustus_model.g2689.t1
Valid prediction for Augustus_model.g2705.t1
Valid prediction for snap_scaffold_2-snap.1506-T1
Valid prediction for GlimmerHMM_glimmerT_4017-T1
Valid prediction for GlimmerHMM_glimmerT_4014-T1
Valid prediction for Augustus_model.g2681.t1
Valid prediction for Augustus_model.g2708.t1
Valid prediction for snap_scaffold_2-snap.1522-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_4015-T1
Valid prediction for GlimmerHMM_glimmerT_4020-T1
Valid prediction for GlimmerHMM_glimmerT_4022-T1
Valid prediction for snap_scaffold_2-snap.1498-T1
Valid prediction for snap_scaffold_2-snap.1502-T1
Valid prediction for GlimmerHMM_glimmerT_4010-T1
Valid prediction for GlimmerHMM_glimmerT_4008-T1
Valid prediction for Augustus_model.g2687.t1
Valid prediction for Augustus_model.g2686.t1
Valid prediction for GlimmerHMM_glimmerT_4007-T1
Valid prediction for GlimmerHMM_glimmerT_4009-T1
Valid prediction for GlimmerHMM_glimmerT_4011-T1
Valid prediction for Augustus_model.g2690.t1
Valid prediction for GlimmerHMM_glimmerT_4033-T1
Valid prediction for GlimmerHMM_glimmerT_4036-T1
Valid prediction for GlimmerHMM_glimmerT_4030-T1
Valid prediction for Augustus_model.g2712.t1

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

-building trellis in range 1 - 232322
-exon list size: 336


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.4    
2.7    
3.0    
3.3    
3.6    
3.8    
4.1    
4.4    
4.7    
5.0    
5.3    
5.6    
5.9    
6.2    
6.5    
6.8    
7.1    
7.4    
7.7    
8.0    
8.3    
8.6    
8.9    
9.2    
9.5    
9.8    
10.1    
10.4    
10.7    
10.9    
11.2    
11.5    
11.8    
12.1    
12.4    
12.7    
13.0    
13.3    
13.6    
13.9    
14.2    
14.5    
14.8    
15.1    
15.4    
15.7    
16.0    
16.3    
16.6    
16.9    
17.2    
17.5    
17.8    
18.0    
18.3    
18.6    
18.9    
19.2    
19.5    
19.8    
20.1    
20.4    
20.7    
21.0    
21.3    
21.6    
21.9    
22.2    
22.5    
22.8    
23.1    
23.4    
23.7    
24.0    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
26.9    
27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
29.0    
29.3    
29.6    
29.9    
30.2    
30.5    
30.8    
31.1    
31.4    
31.7    
32.0    
32.2    
32.5    
32.8    
33.1    
33.4    
33.7    
34.0    
34.3    
34.6    
34.9    
35.2    
35.5    
35.8    
36.1    
36.4    
36.7    
37.0    
37.3    
37.6    
37.9    
38.2    
38.5    
38.8    
39.1    
39.3    
39.6    
39.9    
40.2    
40.5    
40.8    
41.1    
41.4    
41.7    
42.0    
42.3    
42.6    
42.9    
43.2    
43.5    
43.8    
44.1    
44.4    
44.7    
45.0    
45.3    
45.6    
45.9    
46.2    
46.4    
46.7    
47.0    
47.3    
47.6    
47.9    
48.2    
48.5    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.5    
51.8    
52.1    
52.4    
52.7    
53.0    
53.3    
53.6    
53.8    
54.1    
54.4    
54.7    
55.0    
55.3    
55.6    
55.9    
56.2    
56.5    
56.8    
57.1    
57.4    
57.7    
58.0    
58.3    
58.6    
58.9    
59.2    
59.5    
59.8    
60.1    
60.4    
60.7    
60.9    
61.2    
61.5    
61.8    
62.1    
62.4    
62.7    
63.0    
63.3    
63.6    
63.9    
64.2    
64.5    
64.8    
65.1    
65.4    
65.7    
66.0    
66.3    
66.6    
66.9    
67.2    
67.5    
67.8    
68.0    
68.3    
68.6    
68.9    
69.2    
69.5    
69.8    
70.1    
70.4    
70.7    
71.0    
71.3    
71.6    
71.9    
72.2    
72.5    
72.8    
73.1    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
76.0    
76.3    
76.6    
76.9    
77.2    
77.5    
77.8    
78.1    
78.4    
78.7    
79.0    
79.3    
79.6    
79.9    
80.2    
80.5    
80.8    
81.1    
81.4    
81.7    
82.0    
82.2    
82.5    
82.8    
83.1    
83.4    
83.7    
84.0    
84.3    
84.6    
84.9    
85.2    
85.5    
85.8    
86.1    
86.4    
86.7    
87.0    
87.3    
87.6    
87.9    
88.2    
88.5    
88.8    
89.1    
89.3    
89.6    
89.9    
90.2    
90.5    
90.8    
91.1    
91.4    
91.7    
92.0    
92.3    
92.6    
92.9    
93.2    
93.5    
93.8    
94.1    
94.4    
94.7    
95.0    
95.3    
95.6    
95.9    
96.2    
96.4    
96.7    
97.0    
97.3    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 46 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 45 predictions persist after filtering for low support