-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_38

-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 76, 84
Sorry, prediction GeneMark_model.106197_t fails validation.
(AAA)	 AG	76-84	GT	GGG
(AGG)	 AG	144-152	GT	GGG
(AGG)	 AG	301-309	GT	GGG
(AAA)	 AG	369-377	GT	GGG
(AGG)	 AG	527-535	GT	AGG
(AAA)	 AG	652-660	GT	GGG
(GAG)	 AG	865-870	GT	GGG
(AGG)	 AG	912-1004	GT	GGG
(AGG)	 AG	1059-1067	GT	GGG
(AGG)	 AG	1233-1241	GT	GGG
(GAA)	 AG	1424-1435	GT	GGG
(AGG)	 AG	1474-1482	GT	AGG
(AAA)	 AG	1850-1858	GT	GGG
(AAA)	 AG	2060-2068	GT	GGG
(AAA)	 AG	2164-2175	GT	GGG
(AAA)	 AG	2199-2207	GT	GGG
(AAA)	 AG	2397-2405	GT	GGG
(AGG)	 AG	2459-2467	GT	GGG
(AGG)	 AG	2568-2582	GT	GGG
(AGG)	 AG	2630-2638	GT	GGG
(AAA)	 AG	2782-2790	GT	GGG
(AGA)	 AG	2894-2905	GT	AGG
(AAA)	 AG	2937-2949	GG	AGG
-recovered GeneMark_model.106197_t, terminal, 1474, 1482
-recovered GeneMark_model.106197_t, terminal, 2937, 2949
-recovered GeneMark_model.106197_t, internal, 76, 84
-recovered GeneMark_model.106197_t, internal, 144, 152
-recovered GeneMark_model.106197_t, internal, 301, 309
-recovered GeneMark_model.106197_t, internal, 369, 377
-recovered GeneMark_model.106197_t, internal, 527, 535
-recovered GeneMark_model.106197_t, internal, 652, 660
-recovered GeneMark_model.106197_t, internal, 865, 870
-recovered GeneMark_model.106197_t, internal, 912, 1004
-recovered GeneMark_model.106197_t, internal, 1059, 1067
-recovered GeneMark_model.106197_t, internal, 1233, 1241
-recovered GeneMark_model.106197_t, internal, 1424, 1435
-recovered GeneMark_model.106197_t, internal, 1474, 1482
-recovered GeneMark_model.106197_t, internal, 1850, 1858
-recovered GeneMark_model.106197_t, internal, 2060, 2068
-recovered GeneMark_model.106197_t, internal, 2164, 2175
-recovered GeneMark_model.106197_t, internal, 2199, 2207
-recovered GeneMark_model.106197_t, internal, 2397, 2405
-recovered GeneMark_model.106197_t, internal, 2459, 2467
-recovered GeneMark_model.106197_t, internal, 2568, 2582
-recovered GeneMark_model.106197_t, internal, 2630, 2638
-recovered GeneMark_model.106197_t, internal, 2782, 2790
-recovered GeneMark_model.106197_t, internal, 2894, 2905
Valid prediction for GeneMark_model.106200_t
Valid prediction for CodingQuarry_transcript_46465-T1
Valid prediction for HiQ_model.g40576.t1
Couldn't classify 20147, 20383
Sorry, prediction pasa_asmbl_41014.p1 fails validation.
(CAA)	 CC	20147-20383	GT	TGG
(CGT)	 AG	20716-20904	TA	GAT
-recovered pasa_asmbl_41014.p1, terminal, 20716, 20904
Valid prediction for GeneMark_model.106198_t
Valid prediction for GlimmerHMM_glimmerT_60994-T1
Valid prediction for GlimmerHMM_glimmerT_60996-T1
Valid prediction for snap_scaffold_38-snap.1-T1
Valid prediction for Augustus_model.g40577.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_38-snap.3-T1
Valid prediction for GlimmerHMM_glimmerT_60995-T1
Valid prediction for snap_scaffold_38-snap.2-T1
Valid prediction for GeneMark_model.106199_t

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

-building trellis in range 1 - 36188
-exon list size: 87


building trellis

1.1    
2.2    
3.4    
4.5    
5.6    
6.7    
7.9    
9.0    
10.1    
11.2    
12.4    
13.5    
14.6    
15.7    
16.9    
18.0    
19.1    
20.2    
21.3    
22.5    
23.6    
24.7    
25.8    
27.0    
28.1    
29.2    
30.3    
31.5    
32.6    
33.7    
34.8    
36.0    
37.1    
38.2    
39.3    
40.4    
41.6    
42.7    
43.8    
44.9    
46.1    
47.2    
48.3    
49.4    
50.6    
51.7    
52.8    
53.9    
55.1    
56.2    
57.3    
58.4    
59.6    
60.7    
61.8    
62.9    
64.0    
65.2    
66.3    
67.4    
68.5    
69.7    
70.8    
71.9    
73.0    
74.2    
75.3    
76.4    
77.5    
78.7    
79.8    
80.9    
82.0    
83.1    
84.3    
85.4    
86.5    
87.6    
88.8    
89.9    
91.0    
92.1    
93.3    
94.4    
95.5    
96.6    
97.8    
98.9    
-found 2 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 2 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 20287
-exon list size: 62


building trellis

1.6    
3.1    
4.7    
6.2    
7.8    
9.4    
10.9    
12.5    
14.1    
15.6    
17.2    
18.8    
20.3    
21.9    
23.4    
25.0    
26.6    
28.1    
29.7    
31.2    
32.8    
34.4    
35.9    
37.5    
39.1    
40.6    
42.2    
43.8    
45.3    
46.9    
48.4    
50.0    
51.6    
53.1    
54.7    
56.2    
57.8    
59.4    
60.9    
62.5    
64.1    
65.6    
67.2    
68.8    
70.3    
71.9    
73.4    
75.0    
76.6    
78.1    
79.7    
81.2    
82.8    
84.4    
85.9    
87.5    
89.1    
90.6    
92.2    
93.8    
95.3    
96.9    
98.4    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 871 - 20287
-exon list size: 44


building trellis

2.2    
4.3    
6.5    
8.7    
10.9    
13.0    
15.2    
17.4    
19.6    
21.7    
23.9    
26.1    
28.3    
30.4    
32.6    
34.8    
37.0    
39.1    
41.3    
43.5    
45.7    
47.8    
50.0    
52.2    
54.3    
56.5    
58.7    
60.9    
63.0    
65.2    
67.4    
69.6    
71.7    
73.9    
76.1    
78.3    
80.4    
82.6    
84.8    
87.0    
89.1    
91.3    
93.5    
95.7    
97.8    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 2791 - 20287
-exon list size: 9


building trellis

9.1    
18.2    
27.3    
36.4    
45.5    
54.5    
63.6    
72.7    
81.8    
90.9    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 2906 - 20287
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 2950 - 20287
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 2950 - 19412
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 2950 - 15015
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support
	-no exons in range 2950 - 14749