-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_15/scaffold_15_16314642-16416864

-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_38445-T1
Valid prediction for snap_scaffold_15-snap.3227-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GeneMark_model.65893_t
Couldn't classify 36151, 36246
Couldn't classify 39580, 39720
Sorry, prediction pasa_asmbl_14804.p1 fails validation.
(CTC)	 AA	36151-36246	GT	CGG
(GTA)	 AG	36678-36803	GT	AGG
(GAA)	 AG	39580-39720	TA	GGT
-recovered pasa_asmbl_14804.p1, internal, 36678, 36803
Valid prediction for CodingQuarry_transcript_18249-T1
Valid prediction for snap_scaffold_15-snap.3226-T1
Valid prediction for GlimmerHMM_glimmerT_38442-T1
Valid prediction for GlimmerHMM_glimmerT_38446-T1
Valid prediction for GeneMark_model.65891_t
Valid prediction for GlimmerHMM_glimmerT_38444-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_15-snap.3228-T1
Valid prediction for GlimmerHMM_glimmerT_38450-T1
Couldn't classify 43800, 43904
Sorry, prediction pasa_asmbl_14805.p1 fails validation.
(CTC)	 TT	43800-43904	GC	ATG
(GAT)	 AG	44000-44113	GT	AGG
(AAT)	 AG	44204-44310	GT	GTG
(GTA)	 AG	44440-44547	GT	AGG
(GTC)	 AG	46134-46168	GT	TTG
(CTA)	 AG	49041-49219	GT	AGG
(GTG)	 AG	49309-49413	GT	AGG
(GAG)	 AG	49511-49652	GT	AGG
(AGG)	 AG	49736-49856	GT	AGG
(ATT)	 AG	49966-50065	GT	AGG
(CAT)	 AG	50182-50268	GT	AGG
(ATT)	 AG	50391-50450	TA	AAT
-recovered pasa_asmbl_14805.p1, terminal, 50391, 50450
-recovered pasa_asmbl_14805.p1, internal, 44000, 44113
-recovered pasa_asmbl_14805.p1, internal, 44204, 44310
-recovered pasa_asmbl_14805.p1, internal, 44440, 44547
-recovered pasa_asmbl_14805.p1, internal, 46134, 46168
-recovered pasa_asmbl_14805.p1, internal, 49041, 49219
-recovered pasa_asmbl_14805.p1, internal, 49309, 49413
-recovered pasa_asmbl_14805.p1, internal, 49511, 49652
-recovered pasa_asmbl_14805.p1, internal, 49736, 49856
-recovered pasa_asmbl_14805.p1, internal, 49966, 50065
-recovered pasa_asmbl_14805.p1, internal, 50182, 50268
Valid prediction for GlimmerHMM_glimmerT_38453-T1
Valid prediction for snap_scaffold_15-snap.3224-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_15-snap.3225-T1
Couldn't classify 11979, 11996
Sorry, prediction pasa_asmbl_15850.p1 fails validation.
(CTC)	 GA	11979-11996	GT	CTG
(TCT)	 AG	12072-13064	GT	AAG
-recovered pasa_asmbl_15850.p1, terminal, 12072, 13064
-recovered pasa_asmbl_15850.p1, internal, 12072, 13064
Couldn't classify 71196, 72368
Sorry, prediction pasa_asmbl_15842.p1 fails validation.
(AAC)	 CT	71196-72368	GT	TGG
(GTC)	 AG	72908-73035	GT	AGG
(GGT)	 AG	74187-74331	GT	AGG
(TAC)	 AG	76246-76374	GT	AGG
(GTG)	 AG	77581-77790	CA	AGC
add_exon() Sorry, pasa_asmbl_15842.p1 72908-73035-terminal-2 is invalid.
-recovered pasa_asmbl_15842.p1, terminal, 72908, 73035
-recovered pasa_asmbl_15842.p1, terminal, 77581, 77790
-recovered pasa_asmbl_15842.p1, internal, 72908, 73035
-recovered pasa_asmbl_15842.p1, internal, 74187, 74331
-recovered pasa_asmbl_15842.p1, internal, 76246, 76374
Valid prediction for GeneMark_model.65901_t
Valid prediction for snap_scaffold_15-snap.3229-T1
Valid prediction for snap_scaffold_15-snap.3236-T1
Valid prediction for snap_scaffold_15-snap.3237-T1
Valid prediction for snap_scaffold_15-snap.3234-T1
Valid prediction for GlimmerHMM_glimmerT_38447-T1
Valid prediction for GlimmerHMM_glimmerT_38451-T1
Valid prediction for GlimmerHMM_glimmerT_38449-T1
Valid prediction for snap_scaffold_15-snap.3235-T1
Valid prediction for GeneMark_model.65899_t
Valid prediction for GlimmerHMM_glimmerT_38443-T1
Couldn't classify 425, 829
Sorry, prediction GeneMark_model.65902_t fails validation.
(GAG)	 AG	425-829	GT	AGG
(AAC)	 AG	1188-1284	GC	AGG
(GGA)	 AG	1398-1609	GT	GGG
(AGA)	 AG	2316-2499	GT	ATG
(GGA)	 AG	2603-2764	GT	TGG
(GCT)	 AG	2855-2969	GT	GAG
(GGG)	 AG	3441-3545	GT	AGG
(GTA)	 AG	3668-3878	GT	AAG
(AAT)	 AG	4009-4181	GT	TGG
(ACA)	 AG	4306-4469	GT	AGG
(AGT)	 AG	6057-6645	GT	TGG
(GAG)	 AG	6828-6847	AT	AGA
-recovered GeneMark_model.65902_t, terminal, 6828, 6847
-recovered GeneMark_model.65902_t, internal, 425, 829
-recovered GeneMark_model.65902_t, internal, 1188, 1284
-recovered GeneMark_model.65902_t, internal, 1398, 1609
-recovered GeneMark_model.65902_t, internal, 2316, 2499
-recovered GeneMark_model.65902_t, internal, 2603, 2764
-recovered GeneMark_model.65902_t, internal, 2855, 2969
-recovered GeneMark_model.65902_t, internal, 3441, 3545
-recovered GeneMark_model.65902_t, internal, 3668, 3878
-recovered GeneMark_model.65902_t, internal, 4009, 4181
-recovered GeneMark_model.65902_t, internal, 4306, 4469
-recovered GeneMark_model.65902_t, internal, 6057, 6645
Couldn't classify 10164, 10478
Sorry, prediction pasa_asmbl_15912.p1 fails validation.
(TAT)	 TG	10164-10478	AA	ACA
Valid prediction for snap_scaffold_15-snap.3231-T1
Valid prediction for snap_scaffold_15-snap.3232-T1
Valid prediction for GlimmerHMM_glimmerT_38452-T1
Valid prediction for GlimmerHMM_glimmerT_38448-T1
Valid prediction for snap_scaffold_15-snap.3233-T1
Valid prediction for GlimmerHMM_glimmerT_38454-T1
Couldn't classify 70359, 71144
Sorry, prediction pasa_asmbl_15844.p1 fails validation.
(CTA)	 AT	70359-71144	GA	GTG
Valid prediction for GlimmerHMM_glimmerT_38455-T1
Couldn't classify 12072, 13060
Sorry, prediction GlimmerHMM_glimmerT_38456-T1 fails validation.
(TCT)	 AG	12072-13060	GT	CAG
(GTA)	 AG	22061-22163	GT	AAG
(GTT)	 AG	22269-22414	GT	AAG
(ACA)	 AG	22529-22676	GT	TGG
(CCT)	 AG	22835-22987	GT	TGG
(CAC)	 AG	23074-23202	GC	GAG
-recovered GlimmerHMM_glimmerT_38456-T1, terminal, 23074, 23202
-recovered GlimmerHMM_glimmerT_38456-T1, internal, 12072, 13060
-recovered GlimmerHMM_glimmerT_38456-T1, internal, 22061, 22163
-recovered GlimmerHMM_glimmerT_38456-T1, internal, 22269, 22414
-recovered GlimmerHMM_glimmerT_38456-T1, internal, 22529, 22676
-recovered GlimmerHMM_glimmerT_38456-T1, internal, 22835, 22987
-recovered GlimmerHMM_glimmerT_38456-T1, internal, 23074, 23202
Valid prediction for snap_scaffold_15-snap.3230-T1
Valid prediction for GeneMark_model.65896_t
Valid prediction for GeneMark_model.65900_t
Valid prediction for GeneMark_model.65897_t
Valid prediction for GlimmerHMM_glimmerT_38441-T1

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

-building trellis in range 1 - 102223
-exon list size: 206


building trellis

0.5    
1.0    
1.4    
1.9    
2.4    
2.9    
3.4    
3.8    
4.3    
4.8    
5.3    
5.8    
6.2    
6.7    
7.2    
7.7    
8.2    
8.7    
9.1    
9.6    
10.1    
10.6    
11.1    
11.5    
12.0    
12.5    
13.0    
13.5    
13.9    
14.4    
14.9    
15.4    
15.9    
16.3    
16.8    
17.3    
17.8    
18.3    
18.8    
19.2    
19.7    
20.2    
20.7    
21.2    
21.6    
22.1    
22.6    
23.1    
23.6    
24.0    
24.5    
25.0    
25.5    
26.0    
26.4    
26.9    
27.4    
27.9    
28.4    
28.8    
29.3    
29.8    
30.3    
30.8    
31.2    
31.7    
32.2    
32.7    
33.2    
33.7    
34.1    
34.6    
35.1    
35.6    
36.1    
36.5    
37.0    
37.5    
38.0    
38.5    
38.9    
39.4    
39.9    
40.4    
40.9    
41.3    
41.8    
42.3    
42.8    
43.3    
43.8    
44.2    
44.7    
45.2    
45.7    
46.2    
46.6    
47.1    
47.6    
48.1    
48.6    
49.0    
49.5    
50.0    
50.5    
51.0    
51.4    
51.9    
52.4    
52.9    
53.4    
53.8    
54.3    
54.8    
55.3    
55.8    
56.2    
56.7    
57.2    
57.7    
58.2    
58.7    
59.1    
59.6    
60.1    
60.6    
61.1    
61.5    
62.0    
62.5    
63.0    
63.5    
63.9    
64.4    
64.9    
65.4    
65.9    
66.3    
66.8    
67.3    
67.8    
68.3    
68.8    
69.2    
69.7    
70.2    
70.7    
71.2    
71.6    
72.1    
72.6    
73.1    
73.6    
74.0    
74.5    
75.0    
75.5    
76.0    
76.4    
76.9    
77.4    
77.9    
78.4    
78.8    
79.3    
79.8    
80.3    
80.8    
81.2    
81.7    
82.2    
82.7    
83.2    
83.7    
84.1    
84.6    
85.1    
85.6    
86.1    
86.5    
87.0    
87.5    
88.0    
88.5    
88.9    
89.4    
89.9    
90.4    
90.9    
91.3    
91.8    
92.3    
92.8    
93.3    
93.8    
94.2    
94.7    
95.2    
95.7    
96.2    
96.6    
97.1    
97.6    
98.1    
98.6    
99.0    
99.5    
-found 19 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 90153 - 102223
-exon list size: 35


building trellis

2.7    
5.4    
8.1    
10.8    
13.5    
16.2    
18.9    
21.6    
24.3    
27.0    
29.7    
32.4    
35.1    
37.8    
40.5    
43.2    
45.9    
48.6    
51.4    
54.1    
56.8    
59.5    
62.2    
64.9    
67.6    
70.3    
73.0    
75.7    
78.4    
81.1    
83.8    
86.5    
89.2    
91.9    
94.6    
97.3    
-found 3 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 3 predictions persist after filtering for low support