-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_19/scaffold_19_13482737-13612064

-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 GeneMark_model.80576_t
Valid prediction for Augustus_model.g30921.t1
Valid prediction for snap_scaffold_19-snap.2675-T1
Valid prediction for GlimmerHMM_glimmerT_46318-T1
Valid prediction for snap_scaffold_19-snap.2682-T1
Couldn't classify 24307, 24347
Sorry, prediction pasa_asmbl_22688.p1 fails validation.
(TGT)	 TG	24307-24347	GT	ACG
(GAA)	 AG	24594-24666	GT	AGG
(GGT)	 AG	25284-25430	GT	TAG
(GTG)	 AG	25515-25603	GT	GGG
(TGC)	 AG	25719-25876	GT	CGG
(GAG)	 AG	26095-26192	TA	GAT
-recovered pasa_asmbl_22688.p1, terminal, 26095, 26192
-recovered pasa_asmbl_22688.p1, internal, 24594, 24666
-recovered pasa_asmbl_22688.p1, internal, 25284, 25430
-recovered pasa_asmbl_22688.p1, internal, 25515, 25603
-recovered pasa_asmbl_22688.p1, internal, 25719, 25876
Valid prediction for GlimmerHMM_glimmerT_46323-T1
Valid prediction for snap_scaffold_19-snap.2671-T1
Valid prediction for GeneMark_model.80587_t
Valid prediction for GeneMark_model.80592_t
Valid prediction for snap_scaffold_19-snap.2669-T1
Valid prediction for GeneMark_model.80585_t
Valid prediction for GeneMark_model.80580_t
Valid prediction for GlimmerHMM_glimmerT_46325-T1
Valid prediction for GlimmerHMM_glimmerT_46329-T1
Valid prediction for snap_scaffold_19-snap.2677-T1
Valid prediction for snap_scaffold_19-snap.2670-T1
Valid prediction for Augustus_model.g30920.t1
Valid prediction for Augustus_model.g30922.t1
Valid prediction for GeneMark_model.80593_t
Valid prediction for snap_scaffold_19-snap.2667-T1
Valid prediction for GlimmerHMM_glimmerT_46320-T1
Valid prediction for GlimmerHMM_glimmerT_46336-T1
Valid prediction for snap_scaffold_19-snap.2676-T1
Valid prediction for GlimmerHMM_glimmerT_46317-T1
Valid prediction for GeneMark_model.80583_t
Valid prediction for CodingQuarry_transcript_25849-T1
Valid prediction for GlimmerHMM_glimmerT_46328-T1
Valid prediction for Augustus_model.g30923.t1
Couldn't classify 57850, 58221
Sorry, prediction pasa_asmbl_21952.p1 fails validation.
(CTG)	 CT	57850-58221	CG	CTC
Valid prediction for GlimmerHMM_glimmerT_46316-T1
Valid prediction for GlimmerHMM_glimmerT_46330-T1
Valid prediction for snap_scaffold_19-snap.2666-T1
Valid prediction for GlimmerHMM_glimmerT_46338-T1
Valid prediction for GlimmerHMM_glimmerT_46331-T1
Valid prediction for GeneMark_model.80588_t
Valid prediction for GlimmerHMM_glimmerT_46335-T1
Valid prediction for GlimmerHMM_glimmerT_46322-T1
Valid prediction for snap_scaffold_19-snap.2680-T1
Valid prediction for GeneMark_model.80579_t
Valid prediction for snap_scaffold_19-snap.2673-T1
Valid prediction for snap_scaffold_19-snap.2674-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_46321-T1
Valid prediction for GeneMark_model.80578_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 GlimmerHMM_glimmerT_46339-T1
Valid prediction for pasa_asmbl_21876.p1
Valid prediction for GeneMark_model.80581_t
Valid prediction for snap_scaffold_19-snap.2672-T1
Valid prediction for GeneMark_model.80582_t
Valid prediction for GlimmerHMM_glimmerT_46319-T1
Valid prediction for GeneMark_model.80590_t
Valid prediction for GlimmerHMM_glimmerT_46333-T1
Valid prediction for snap_scaffold_19-snap.2668-T1
Valid prediction for GlimmerHMM_glimmerT_46327-T1
Valid prediction for snap_scaffold_19-snap.2664-T1
Valid prediction for snap_scaffold_19-snap.2683-T1
Valid prediction for GlimmerHMM_glimmerT_46326-T1
Valid prediction for snap_scaffold_19-snap.2678-T1
Valid prediction for Augustus_model.g30919.t1
Valid prediction for GlimmerHMM_glimmerT_46324-T1
Valid prediction for GeneMark_model.80589_t
Valid prediction for GlimmerHMM_glimmerT_46337-T1
Valid prediction for GlimmerHMM_glimmerT_46334-T1
Valid prediction for GlimmerHMM_glimmerT_46315-T1
Valid prediction for snap_scaffold_19-snap.2679-T1
Valid prediction for GeneMark_model.80577_t
Valid prediction for snap_scaffold_19-snap.2681-T1
Valid prediction for snap_scaffold_19-snap.2665-T1
Valid prediction for GeneMark_model.80584_t
Valid prediction for GlimmerHMM_glimmerT_46332-T1
Valid prediction for HiQ_model.g30924.t1

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

-building trellis in range 1 - 129328
-exon list size: 186


building trellis

0.5    
1.1    
1.6    
2.1    
2.7    
3.2    
3.7    
4.3    
4.8    
5.3    
5.9    
6.4    
6.9    
7.4    
8.0    
8.5    
9.0    
9.6    
10.1    
10.6    
11.2    
11.7    
12.2    
12.8    
13.3    
13.8    
14.4    
14.9    
15.4    
16.0    
16.5    
17.0    
17.6    
18.1    
18.6    
19.1    
19.7    
20.2    
20.7    
21.3    
21.8    
22.3    
22.9    
23.4    
23.9    
24.5    
25.0    
25.5    
26.1    
26.6    
27.1    
27.7    
28.2    
28.7    
29.3    
29.8    
30.3    
30.9    
31.4    
31.9    
32.4    
33.0    
33.5    
34.0    
34.6    
35.1    
35.6    
36.2    
36.7    
37.2    
37.8    
38.3    
38.8    
39.4    
39.9    
40.4    
41.0    
41.5    
42.0    
42.6    
43.1    
43.6    
44.1    
44.7    
45.2    
45.7    
46.3    
46.8    
47.3    
47.9    
48.4    
48.9    
49.5    
50.0    
50.5    
51.1    
51.6    
52.1    
52.7    
53.2    
53.7    
54.3    
54.8    
55.3    
55.9    
56.4    
56.9    
57.4    
58.0    
58.5    
59.0    
59.6    
60.1    
60.6    
61.2    
61.7    
62.2    
62.8    
63.3    
63.8    
64.4    
64.9    
65.4    
66.0    
66.5    
67.0    
67.6    
68.1    
68.6    
69.1    
69.7    
70.2    
70.7    
71.3    
71.8    
72.3    
72.9    
73.4    
73.9    
74.5    
75.0    
75.5    
76.1    
76.6    
77.1    
77.7    
78.2    
78.7    
79.3    
79.8    
80.3    
80.9    
81.4    
81.9    
82.4    
83.0    
83.5    
84.0    
84.6    
85.1    
85.6    
86.2    
86.7    
87.2    
87.8    
88.3    
88.8    
89.4    
89.9    
90.4    
91.0    
91.5    
92.0    
92.6    
93.1    
93.6    
94.1    
94.7    
95.2    
95.7    
96.3    
96.8    
97.3    
97.9    
98.4    
98.9    
99.5    
-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