-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_19548774-19661999

-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 70977, 71188
Couldn't classify 73570, 73668
Sorry, prediction pasa_asmbl_46325.p1 fails validation.
(AGT)	 AC	70977-71188	GT	AGG
(CTG)	 AG	72651-72766	GT	AGG
(GCA)	 AG	73068-73195	GT	AGG
(GAT)	 AG	73570-73668	GT	AGG
add_exon() Sorry, pasa_asmbl_46325.p1 72651-72766-terminal-2 is invalid.
-recovered pasa_asmbl_46325.p1, terminal, 72651, 72766
-recovered pasa_asmbl_46325.p1, internal, 72651, 72766
-recovered pasa_asmbl_46325.p1, internal, 73068, 73195
-recovered pasa_asmbl_46325.p1, internal, 73570, 73668
Valid prediction for snap_scaffold_5-snap.3659-T1
Valid prediction for GlimmerHMM_glimmerT_13850-T1
Valid prediction for snap_scaffold_5-snap.3663-T1
Valid prediction for GlimmerHMM_glimmerT_13855-T1
Valid prediction for GlimmerHMM_glimmerT_13860-T1
Valid prediction for snap_scaffold_5-snap.3653-T1
Sorry, intron length (9) is less than minimum required (10)
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_5-snap.3665-T1
Valid prediction for GlimmerHMM_glimmerT_13857-T1
Valid prediction for GlimmerHMM_glimmerT_13849-T1
Valid prediction for snap_scaffold_5-snap.3667-T1
Couldn't classify 53123, 53288
Couldn't classify 59805, 59893
Sorry, prediction pasa_asmbl_46323.p1 fails validation.
(GAG)	 AC	53123-53288	GT	CAG
(ATG)	 AG	54010-54125	GT	AGG
(GTT)	 AG	56125-56250	GT	AAG
(CAT)	 AG	59024-59159	GT	GGG
(GTT)	 AG	59805-59893	AG	CCA
add_exon() Sorry, pasa_asmbl_46323.p1 54010-54125-initial-1 is invalid.
-recovered pasa_asmbl_46323.p1, initial, 54010, 54125
-recovered pasa_asmbl_46323.p1, internal, 54010, 54125
-recovered pasa_asmbl_46323.p1, internal, 56125, 56250
-recovered pasa_asmbl_46323.p1, internal, 59024, 59159
Valid prediction for GlimmerHMM_glimmerT_13852-T1
Valid prediction for GlimmerHMM_glimmerT_13858-T1
Valid prediction for GlimmerHMM_glimmerT_13851-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_5-snap.3655-T1
Valid prediction for GlimmerHMM_glimmerT_13856-T1
Valid prediction for snap_scaffold_5-snap.3654-T1
Valid prediction for snap_scaffold_5-snap.3662-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_13847-T1
Valid prediction for GlimmerHMM_glimmerT_13848-T1
Valid prediction for snap_scaffold_5-snap.3666-T1
Valid prediction for GlimmerHMM_glimmerT_13854-T1
Valid prediction for snap_scaffold_5-snap.3664-T1
Valid prediction for GlimmerHMM_glimmerT_13859-T1
Valid prediction for snap_scaffold_5-snap.3657-T1
Valid prediction for snap_scaffold_5-snap.3660-T1
Valid prediction for snap_scaffold_5-snap.3658-T1
Sorry, intron length (8) is less than minimum required (10)
Couldn't classify 76422, 76454
Sorry, prediction pasa_asmbl_44921.p1 fails validation.
(ATT)	 CT	76422-76454	GT	AGG
(GTG)	 AG	76534-76601	GT	AGG
(GTG)	 AG	76722-77090	GT	AGG
(ATT)	 AG	78378-78630	TG	AGT
-recovered pasa_asmbl_44921.p1, terminal, 78378, 78630
-recovered pasa_asmbl_44921.p1, internal, 76534, 76601
-recovered pasa_asmbl_44921.p1, internal, 76722, 77090
Valid prediction for snap_scaffold_5-snap.3656-T1
Valid prediction for GlimmerHMM_glimmerT_13846-T1
Valid prediction for GlimmerHMM_glimmerT_13853-T1
Valid prediction for snap_scaffold_5-snap.3661-T1

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

-building trellis in range 1 - 113226
-exon list size: 100


building trellis

1.0    
2.0    
2.9    
3.9    
4.9    
5.9    
6.9    
7.8    
8.8    
9.8    
10.8    
11.8    
12.7    
13.7    
14.7    
15.7    
16.7    
17.6    
18.6    
19.6    
20.6    
21.6    
22.5    
23.5    
24.5    
25.5    
26.5    
27.5    
28.4    
29.4    
30.4    
31.4    
32.4    
33.3    
34.3    
35.3    
36.3    
37.3    
38.2    
39.2    
40.2    
41.2    
42.2    
43.1    
44.1    
45.1    
46.1    
47.1    
48.0    
49.0    
50.0    
51.0    
52.0    
52.9    
53.9    
54.9    
55.9    
56.9    
57.8    
58.8    
59.8    
60.8    
61.8    
62.7    
63.7    
64.7    
65.7    
66.7    
67.6    
68.6    
69.6    
70.6    
71.6    
72.5    
73.5    
74.5    
75.5    
76.5    
77.5    
78.4    
79.4    
80.4    
81.4    
82.4    
83.3    
84.3    
85.3    
86.3    
87.3    
88.2    
89.2    
90.2    
91.2    
92.2    
93.1    
94.1    
95.1    
96.1    
97.1    
98.0    
99.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 54009
-exon list size: 39


building trellis

2.4    
4.9    
7.3    
9.8    
12.2    
14.6    
17.1    
19.5    
22.0    
24.4    
26.8    
29.3    
31.7    
34.1    
36.6    
39.0    
41.5    
43.9    
46.3    
48.8    
51.2    
53.7    
56.1    
58.5    
61.0    
63.4    
65.9    
68.3    
70.7    
73.2    
75.6    
78.0    
80.5    
82.9    
85.4    
87.8    
90.2    
92.7    
95.1    
97.6    
-found 5 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 5 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 36694 - 54009
-exon list size: 13


building trellis

6.7    
13.3    
20.0    
26.7    
33.3    
40.0    
46.7    
53.3    
60.0    
66.7    
73.3    
80.0    
86.7    
93.3    
-found 4 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 59160 - 113226
-exon list size: 57


building trellis

1.7    
3.4    
5.1    
6.8    
8.5    
10.2    
11.9    
13.6    
15.3    
16.9    
18.6    
20.3    
22.0    
23.7    
25.4    
27.1    
28.8    
30.5    
32.2    
33.9    
35.6    
37.3    
39.0    
40.7    
42.4    
44.1    
45.8    
47.5    
49.2    
50.8    
52.5    
54.2    
55.9    
57.6    
59.3    
61.0    
62.7    
64.4    
66.1    
67.8    
69.5    
71.2    
72.9    
74.6    
76.3    
78.0    
79.7    
81.4    
83.1    
84.7    
86.4    
88.1    
89.8    
91.5    
93.2    
94.9    
96.6    
98.3    
-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 73669 - 113226
-exon list size: 40


building trellis

2.4    
4.8    
7.1    
9.5    
11.9    
14.3    
16.7    
19.0    
21.4    
23.8    
26.2    
28.6    
31.0    
33.3    
35.7    
38.1    
40.5    
42.9    
45.2    
47.6    
50.0    
52.4    
54.8    
57.1    
59.5    
61.9    
64.3    
66.7    
69.0    
71.4    
73.8    
76.2    
78.6    
81.0    
83.3    
85.7    
88.1    
90.5    
92.9    
95.2    
97.6    
-found 6 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 5 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 102109 - 113226
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal

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