-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_8468997-8805476

-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 GlimmerHMM_glimmerT_22598-T1
Valid prediction for Augustus_model.g15032.t1
Valid prediction for snap_scaffold_9-snap.1775-T1
Valid prediction for Augustus_model.g15040.t1
Valid prediction for snap_scaffold_9-snap.1772-T1
Valid prediction for GlimmerHMM_glimmerT_22593-T1
Valid prediction for Augustus_model.g15035.t1
Valid prediction for GlimmerHMM_glimmerT_22600-T1
Valid prediction for snap_scaffold_9-snap.1771-T1
Valid prediction for snap_scaffold_9-snap.1764-T1
Valid prediction for GlimmerHMM_glimmerT_22587-T1
Valid prediction for Augustus_model.g15038.t1
Valid prediction for GlimmerHMM_glimmerT_22595-T1
Valid prediction for Augustus_model.g15039.t1
Valid prediction for snap_scaffold_9-snap.1760-T1
Valid prediction for GlimmerHMM_glimmerT_22604-T1
Valid prediction for snap_scaffold_9-snap.1773-T1
Valid prediction for snap_scaffold_9-snap.1768-T1
Valid prediction for snap_scaffold_9-snap.1756-T1
Valid prediction for GlimmerHMM_glimmerT_22592-T1
Valid prediction for GlimmerHMM_glimmerT_22596-T1
Valid prediction for snap_scaffold_9-snap.1774-T1
Valid prediction for GlimmerHMM_glimmerT_22586-T1
Valid prediction for snap_scaffold_9-snap.1755-T1
Valid prediction for snap_scaffold_9-snap.1766-T1
Valid prediction for snap_scaffold_9-snap.1770-T1
Valid prediction for snap_scaffold_9-snap.1765-T1
Valid prediction for Augustus_model.g15037.t1
Valid prediction for snap_scaffold_9-snap.1776-T1
Valid prediction for GlimmerHMM_glimmerT_22583-T1
Valid prediction for GlimmerHMM_glimmerT_22599-T1
Couldn't classify 114284, 114380
Sorry, prediction pasa_asmbl_54176.p1 fails validation.
(GCT)	 CA	114284-114380	GT	AGG
(ATG)	 AG	114605-114642	GT	TGG
(CTC)	 AG	116606-116734	GT	AGG
(GTG)	 AG	117779-117976	AA	AGA
-recovered pasa_asmbl_54176.p1, initial, 114605, 114642
-recovered pasa_asmbl_54176.p1, terminal, 117779, 117976
-recovered pasa_asmbl_54176.p1, internal, 114605, 114642
-recovered pasa_asmbl_54176.p1, internal, 116606, 116734
Valid prediction for Augustus_model.g15036.t1
Valid prediction for GlimmerHMM_glimmerT_22589-T1
Valid prediction for snap_scaffold_9-snap.1761-T1
Valid prediction for GlimmerHMM_glimmerT_22603-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.g15031.t1
Valid prediction for snap_scaffold_9-snap.1777-T1
Valid prediction for Augustus_model.g15028.t1
Valid prediction for GlimmerHMM_glimmerT_22590-T1
Valid prediction for Augustus_model.g15034.t1
Valid prediction for pasa_asmbl_55136.p1
Valid prediction for snap_scaffold_9-snap.1752-T1
Valid prediction for HiQ_model.g15033.t1
Valid prediction for GlimmerHMM_glimmerT_22582-T1
Valid prediction for snap_scaffold_9-snap.1763-T1
Valid prediction for GlimmerHMM_glimmerT_22585-T1
Valid prediction for GlimmerHMM_glimmerT_22601-T1
Valid prediction for snap_scaffold_9-snap.1748-T1
Couldn't classify 308211, 308318
Couldn't classify 308869, 308981
Sorry, prediction pasa_asmbl_55810.p1 fails validation.
(CCG)	 AG	308211-308318	GT	AAG
(GTG)	 AG	308490-308676	GT	CCG
(CTC)	 AG	308869-308981	GT	CGG
-recovered pasa_asmbl_55810.p1, internal, 308211, 308318
-recovered pasa_asmbl_55810.p1, internal, 308490, 308676
-recovered pasa_asmbl_55810.p1, internal, 308869, 308981
Valid prediction for CodingQuarry_transcript_62247-T1
Valid prediction for GlimmerHMM_glimmerT_22602-T1
Valid prediction for snap_scaffold_9-snap.1758-T1
Valid prediction for snap_scaffold_9-snap.1751-T1
Valid prediction for snap_scaffold_9-snap.1767-T1
Valid prediction for snap_scaffold_9-snap.1749-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_22591-T1
Valid prediction for snap_scaffold_9-snap.1757-T1
Valid prediction for snap_scaffold_9-snap.1753-T1
Valid prediction for GlimmerHMM_glimmerT_22584-T1
Valid prediction for GlimmerHMM_glimmerT_22588-T1
Valid prediction for snap_scaffold_9-snap.1769-T1
Valid prediction for GlimmerHMM_glimmerT_22597-T1
Valid prediction for snap_scaffold_9-snap.1750-T1
Valid prediction for snap_scaffold_9-snap.1754-T1
Valid prediction for CodingQuarry_transcript_62246-T1
Valid prediction for Augustus_model.g15029.t1
Valid prediction for CodingQuarry_transcript_62245-T1
Couldn't classify 297951, 298025
Couldn't classify 304041, 304072
Sorry, prediction pasa_asmbl_55134.p1 fails validation.
(GCT)	 TG	297951-298025	GT	CAG
(CAG)	 AG	300310-300430	GT	AGG
(GTC)	 AG	301720-301878	GT	AGG
(ACC)	 AG	303166-303315	GT	AGG
(TGC)	 AG	304041-304072	GG	GGG
-recovered pasa_asmbl_55134.p1, internal, 300310, 300430
-recovered pasa_asmbl_55134.p1, internal, 301720, 301878
-recovered pasa_asmbl_55134.p1, internal, 303166, 303315
Valid prediction for snap_scaffold_9-snap.1759-T1
Valid prediction for GlimmerHMM_glimmerT_22594-T1
Valid prediction for Augustus_model.g15030.t1
Valid prediction for snap_scaffold_9-snap.1762-T1

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

-building trellis in range 1 - 336480
-exon list size: 214


building trellis

0.5    
0.9    
1.4    
1.9    
2.3    
2.8    
3.2    
3.7    
4.2    
4.6    
5.1    
5.6    
6.0    
6.5    
6.9    
7.4    
7.9    
8.3    
8.8    
9.3    
9.7    
10.2    
10.6    
11.1    
11.6    
12.0    
12.5    
13.0    
13.4    
13.9    
14.4    
14.8    
15.3    
15.7    
16.2    
16.7    
17.1    
17.6    
18.1    
18.5    
19.0    
19.4    
19.9    
20.4    
20.8    
21.3    
21.8    
22.2    
22.7    
23.1    
23.6    
24.1    
24.5    
25.0    
25.5    
25.9    
26.4    
26.9    
27.3    
27.8    
28.2    
28.7    
29.2    
29.6    
30.1    
30.6    
31.0    
31.5    
31.9    
32.4    
32.9    
33.3    
33.8    
34.3    
34.7    
35.2    
35.6    
36.1    
36.6    
37.0    
37.5    
38.0    
38.4    
38.9    
39.4    
39.8    
40.3    
40.7    
41.2    
41.7    
42.1    
42.6    
43.1    
43.5    
44.0    
44.4    
44.9    
45.4    
45.8    
46.3    
46.8    
47.2    
47.7    
48.1    
48.6    
49.1    
49.5    
50.0    
50.5    
50.9    
51.4    
51.9    
52.3    
52.8    
53.2    
53.7    
54.2    
54.6    
55.1    
55.6    
56.0    
56.5    
56.9    
57.4    
57.9    
58.3    
58.8    
59.3    
59.7    
60.2    
60.6    
61.1    
61.6    
62.0    
62.5    
63.0    
63.4    
63.9    
64.4    
64.8    
65.3    
65.7    
66.2    
66.7    
67.1    
67.6    
68.1    
68.5    
69.0    
69.4    
69.9    
70.4    
70.8    
71.3    
71.8    
72.2    
72.7    
73.1    
73.6    
74.1    
74.5    
75.0    
75.5    
75.9    
76.4    
76.9    
77.3    
77.8    
78.2    
78.7    
79.2    
79.6    
80.1    
80.6    
81.0    
81.5    
81.9    
82.4    
82.9    
83.3    
83.8    
84.3    
84.7    
85.2    
85.6    
86.1    
86.6    
87.0    
87.5    
88.0    
88.4    
88.9    
89.4    
89.8    
90.3    
90.7    
91.2    
91.7    
92.1    
92.6    
93.1    
93.5    
94.0    
94.4    
94.9    
95.4    
95.8    
96.3    
96.8    
97.2    
97.7    
98.1    
98.6    
99.1    
99.5    
-found 26 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support