-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_8/scaffold_8_18489238-18638009

-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 50853, 50990
Sorry, prediction pasa_asmbl_52556.p1 fails validation.
(AGG)	 CT	50853-50990	GT	AGG
(AAG)	 AG	52390-52582	GT	GGG
(AGG)	 AG	53524-53621	GT	AGG
(GAA)	 AG	54051-54164	AT	GAA
-recovered pasa_asmbl_52556.p1, terminal, 54051, 54164
-recovered pasa_asmbl_52556.p1, internal, 52390, 52582
-recovered pasa_asmbl_52556.p1, internal, 53524, 53621
Valid prediction for GeneMark_model.37211_t
Valid prediction for GeneMark_model.37197_t
Valid prediction for GlimmerHMM_glimmerT_21885-T1
Valid prediction for GeneMark_model.37207_t
Valid prediction for GeneMark_model.37206_t
Valid prediction for snap_scaffold_8-snap.3413-T1
Valid prediction for GeneMark_model.37200_t
Valid prediction for pasa_asmbl_52559.p1
Valid prediction for GeneMark_model.37208_t
Valid prediction for GlimmerHMM_glimmerT_21881-T1
Valid prediction for GlimmerHMM_glimmerT_21878-T1
Valid prediction for CodingQuarry_transcript_59817-T1
Valid prediction for GlimmerHMM_glimmerT_21882-T1
Valid prediction for Augustus_model.g14672.t1
Valid prediction for GlimmerHMM_glimmerT_21880-T1
Valid prediction for snap_scaffold_8-snap.3414-T1
Couldn't classify 45005, 45153
Couldn't classify 45680, 45815
Sorry, prediction pasa_asmbl_52555.p1 fails validation.
(AAC)	 AG	45005-45153	GT	AGG
(ACC)	 AG	45250-45334	GT	AGG
(GTG)	 AG	45410-45504	GT	AGG
(CAT)	 AG	45680-45815	TA	GGT
-recovered pasa_asmbl_52555.p1, internal, 45005, 45153
-recovered pasa_asmbl_52555.p1, internal, 45250, 45334
-recovered pasa_asmbl_52555.p1, internal, 45410, 45504
Valid prediction for snap_scaffold_8-snap.3416-T1
Valid prediction for GlimmerHMM_glimmerT_21895-T1
Valid prediction for snap_scaffold_8-snap.3431-T1
Valid prediction for GlimmerHMM_glimmerT_21896-T1
Valid prediction for GeneMark_model.37210_t
Valid prediction for snap_scaffold_8-snap.3430-T1
Valid prediction for CodingQuarry_transcript_59818-T1
Valid prediction for GlimmerHMM_glimmerT_21898-T1
Valid prediction for GlimmerHMM_glimmerT_21883-T1
Valid prediction for snap_scaffold_8-snap.3417-T1
Valid prediction for GeneMark_model.37205_t
Couldn't classify 27173, 27904
Sorry, prediction pasa_asmbl_52553.p1 fails validation.
(GCA)	 AC	27173-27904	TG	GAT
Valid prediction for GlimmerHMM_glimmerT_21879-T1
Valid prediction for snap_scaffold_8-snap.3415-T1
Valid prediction for snap_scaffold_8-snap.3427-T1
Valid prediction for GeneMark_model.37198_t
Valid prediction for GeneMark_model.37196_t
Valid prediction for snap_scaffold_8-snap.3412-T1
Couldn't classify 91466, 91918
Sorry, prediction pasa_asmbl_53572.p1 fails validation.
(ATG)	 AA	91466-91918	AT	GTA
Valid prediction for GlimmerHMM_glimmerT_21899-T1
Couldn't classify 39598, 39692
Sorry, prediction pasa_asmbl_52554.p1 fails validation.
(ATG)	 AA	37548-37608	GT	AGG
(TGG)	 AG	37860-37999	GT	AGG
(GAG)	 AG	38245-38507	GT	AGG
(TGA)	 AG	38611-38813	GT	AGG
(GGT)	 AG	39412-39516	GT	AGG
(GAA)	 AG	39598-39692	GT	TGG
-recovered pasa_asmbl_52554.p1, initial, 37548, 37608
-recovered pasa_asmbl_52554.p1, internal, 37860, 37999
-recovered pasa_asmbl_52554.p1, internal, 38245, 38507
-recovered pasa_asmbl_52554.p1, internal, 38611, 38813
-recovered pasa_asmbl_52554.p1, internal, 39412, 39516
-recovered pasa_asmbl_52554.p1, internal, 39598, 39692
Valid prediction for GlimmerHMM_glimmerT_21894-T1
Valid prediction for GlimmerHMM_glimmerT_21889-T1
Valid prediction for GeneMark_model.37193_t

-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_8-snap.3428-T1
Valid prediction for GlimmerHMM_glimmerT_21888-T1
Valid prediction for GeneMark_model.37201_t
Valid prediction for GlimmerHMM_glimmerT_21876-T1
Valid prediction for snap_scaffold_8-snap.3432-T1
Valid prediction for snap_scaffold_8-snap.3425-T1
Valid prediction for GlimmerHMM_glimmerT_21900-T1
Valid prediction for snap_scaffold_8-snap.3421-T1
Valid prediction for GlimmerHMM_glimmerT_21892-T1
Couldn't classify 82063, 82271
Sorry, prediction pasa_asmbl_53561.p1 fails validation.
(TTT)	 TC	82063-82271	GT	AGG
(GTA)	 AG	82380-82497	GT	AGG
(GTT)	 AG	85412-86500	AC	AAA
-recovered pasa_asmbl_53561.p1, terminal, 85412, 86500
-recovered pasa_asmbl_53561.p1, internal, 82380, 82497
Couldn't classify 56403, 56732
Sorry, prediction pasa_asmbl_52561.p1 fails validation.
(GTG)	 TC	56403-56732	GG	GCG
Valid prediction for GlimmerHMM_glimmerT_21877-T1
Valid prediction for GlimmerHMM_glimmerT_21884-T1
Valid prediction for snap_scaffold_8-snap.3420-T1
Couldn't classify 75499, 75665
Couldn't classify 76487, 76525
Sorry, prediction CodingQuarry_transcript_59819-T1 fails validation.
(ATG)	 AC	75040-75097	GT	AGG
(GTG)	 AG	75499-75665	GA	GTG
(TTT)	 GG	76487-76525	GG	AAG
-recovered CodingQuarry_transcript_59819-T1, initial, 75040, 75097
Valid prediction for snap_scaffold_8-snap.3422-T1
Valid prediction for snap_scaffold_8-snap.3424-T1
Couldn't classify 59615, 60076
Sorry, prediction pasa_asmbl_53571.p1 fails validation.
(CTC)	 GG	59615-60076	AG	GAA
Valid prediction for GeneMark_model.37203_t
Valid prediction for snap_scaffold_8-snap.3410-T1
Valid prediction for GlimmerHMM_glimmerT_21891-T1
Valid prediction for GeneMark_model.37199_t
Valid prediction for snap_scaffold_8-snap.3429-T1
Valid prediction for GeneMark_model.37204_t
Valid prediction for GeneMark_model.37194_t
Valid prediction for snap_scaffold_8-snap.3419-T1
Valid prediction for snap_scaffold_8-snap.3411-T1
Valid prediction for snap_scaffold_8-snap.3418-T1
Valid prediction for Augustus_model.g14671.t1
Valid prediction for GlimmerHMM_glimmerT_21893-T1
Valid prediction for GlimmerHMM_glimmerT_21886-T1
Valid prediction for pasa_asmbl_53568.p1
Valid prediction for GlimmerHMM_glimmerT_21890-T1
Valid prediction for snap_scaffold_8-snap.3423-T1
Valid prediction for CodingQuarry_transcript_59820-T1
Couldn't classify 74959, 75097
Sorry, prediction pasa_asmbl_53567.p1 fails validation.
(CTC)	 AT	74959-75097	GT	AGG
(GTG)	 AG	75499-75683	AA	AAA
-recovered pasa_asmbl_53567.p1, terminal, 75499, 75683
Valid prediction for snap_scaffold_8-snap.3409-T1
Valid prediction for GeneMark_model.37209_t
Valid prediction for GlimmerHMM_glimmerT_21887-T1
Valid prediction for snap_scaffold_8-snap.3426-T1
Valid prediction for GlimmerHMM_glimmerT_21897-T1
Valid prediction for GeneMark_model.37192_t
Valid prediction for CodingQuarry_transcript_59821-T1

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

-building trellis in range 1 - 148772
-exon list size: 224


building trellis

0.4    
0.9    
1.3    
1.8    
2.2    
2.7    
3.1    
3.5    
4.0    
4.4    
4.9    
5.3    
5.8    
6.2    
6.6    
7.1    
7.5    
8.0    
8.4    
8.8    
9.3    
9.7    
10.2    
10.6    
11.1    
11.5    
11.9    
12.4    
12.8    
13.3    
13.7    
14.2    
14.6    
15.0    
15.5    
15.9    
16.4    
16.8    
17.3    
17.7    
18.1    
18.6    
19.0    
19.5    
19.9    
20.4    
20.8    
21.2    
21.7    
22.1    
22.6    
23.0    
23.5    
23.9    
24.3    
24.8    
25.2    
25.7    
26.1    
26.5    
27.0    
27.4    
27.9    
28.3    
28.8    
29.2    
29.6    
30.1    
30.5    
31.0    
31.4    
31.9    
32.3    
32.7    
33.2    
33.6    
34.1    
34.5    
35.0    
35.4    
35.8    
36.3    
36.7    
37.2    
37.6    
38.1    
38.5    
38.9    
39.4    
39.8    
40.3    
40.7    
41.2    
41.6    
42.0    
42.5    
42.9    
43.4    
43.8    
44.2    
44.7    
45.1    
45.6    
46.0    
46.5    
46.9    
47.3    
47.8    
48.2    
48.7    
49.1    
49.6    
50.0    
50.4    
50.9    
51.3    
51.8    
52.2    
52.7    
53.1    
53.5    
54.0    
54.4    
54.9    
55.3    
55.8    
56.2    
56.6    
57.1    
57.5    
58.0    
58.4    
58.8    
59.3    
59.7    
60.2    
60.6    
61.1    
61.5    
61.9    
62.4    
62.8    
63.3    
63.7    
64.2    
64.6    
65.0    
65.5    
65.9    
66.4    
66.8    
67.3    
67.7    
68.1    
68.6    
69.0    
69.5    
69.9    
70.4    
70.8    
71.2    
71.7    
72.1    
72.6    
73.0    
73.5    
73.9    
74.3    
74.8    
75.2    
75.7    
76.1    
76.5    
77.0    
77.4    
77.9    
78.3    
78.8    
79.2    
79.6    
80.1    
80.5    
81.0    
81.4    
81.9    
82.3    
82.7    
83.2    
83.6    
84.1    
84.5    
85.0    
85.4    
85.8    
86.3    
86.7    
87.2    
87.6    
88.1    
88.5    
88.9    
89.4    
89.8    
90.3    
90.7    
91.2    
91.6    
92.0    
92.5    
92.9    
93.4    
93.8    
94.2    
94.7    
95.1    
95.6    
96.0    
96.5    
96.9    
97.3    
97.8    
98.2    
98.7    
99.1    
99.6    
-found 23 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support