-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_12281428-12447196

-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.26827_t
Valid prediction for GlimmerHMM_glimmerT_15998-T1
Valid prediction for Augustus_model.g10745.t1
Valid prediction for GlimmerHMM_glimmerT_15994-T1
Valid prediction for GlimmerHMM_glimmerT_16001-T1
Valid prediction for snap_scaffold_6-snap.2593-T1
Valid prediction for Augustus_model.g10750.t1
Valid prediction for snap_scaffold_6-snap.2578-T1
Valid prediction for GeneMark_model.26818_t
Valid prediction for GlimmerHMM_glimmerT_15999-T1
Valid prediction for snap_scaffold_6-snap.2591-T1
Valid prediction for HiQ_model.g10741.t1
Valid prediction for Augustus_model.g10743.t1
Valid prediction for GlimmerHMM_glimmerT_15987-T1
Valid prediction for Augustus_model.g10734.t1
Valid prediction for GlimmerHMM_glimmerT_15993-T1
Valid prediction for GlimmerHMM_glimmerT_16011-T1
Valid prediction for snap_scaffold_6-snap.2588-T1
Valid prediction for snap_scaffold_6-snap.2595-T1
Valid prediction for pasa_asmbl_47329.p1
Valid prediction for snap_scaffold_6-snap.2574-T1
Valid prediction for snap_scaffold_6-snap.2599-T1
Valid prediction for GlimmerHMM_glimmerT_16008-T1
Valid prediction for snap_scaffold_6-snap.2582-T1
Valid prediction for GeneMark_model.26829_t
Valid prediction for snap_scaffold_6-snap.2590-T1
Valid prediction for Augustus_model.g10748.t1
Valid prediction for snap_scaffold_6-snap.2596-T1
Valid prediction for snap_scaffold_6-snap.2583-T1
Valid prediction for snap_scaffold_6-snap.2579-T1
Valid prediction for GlimmerHMM_glimmerT_16000-T1
Valid prediction for GeneMark_model.26813_t
Valid prediction for GeneMark_model.26819_t
Valid prediction for HiQ_model.g10738.t1
Valid prediction for Augustus_model.g10731.t1
Valid prediction for GlimmerHMM_glimmerT_16004-T1
Valid prediction for GeneMark_model.26823_t
Valid prediction for GlimmerHMM_glimmerT_16002-T1
Valid prediction for GlimmerHMM_glimmerT_16010-T1
Valid prediction for Augustus_model.g10728.t1
Valid prediction for snap_scaffold_6-snap.2586-T1
Valid prediction for snap_scaffold_6-snap.2573-T1
Valid prediction for snap_scaffold_6-snap.2606-T1
Valid prediction for Augustus_model.g10733.t1
Valid prediction for GeneMark_model.26826_t
Valid prediction for GlimmerHMM_glimmerT_15996-T1
Valid prediction for GeneMark_model.26808_t
Valid prediction for GlimmerHMM_glimmerT_15986-T1
Valid prediction for GlimmerHMM_glimmerT_15991-T1
Valid prediction for GeneMark_model.26820_t
Valid prediction for GeneMark_model.26831_t
Valid prediction for GlimmerHMM_glimmerT_16005-T1
Couldn't classify 87981, 88139
Couldn't classify 89110, 89222
Sorry, prediction pasa_asmbl_47328.p1 fails validation.
(CCA)	 CT	87981-88139	GT	AGG
(GAC)	 AG	88815-88938	GT	TGG
(GGA)	 AG	89110-89222	GG	GAG
-recovered pasa_asmbl_47328.p1, internal, 88815, 88938
Valid prediction for snap_scaffold_6-snap.2597-T1
Valid prediction for GeneMark_model.26815_t
Valid prediction for GlimmerHMM_glimmerT_16006-T1
Valid prediction for CodingQuarry_transcript_55100-T1
Valid prediction for Augustus_model.g10739.t1
Valid prediction for HiQ_model.g10742.t1
Valid prediction for snap_scaffold_6-snap.2601-T1
Valid prediction for Augustus_model.g10727.t1
Valid prediction for snap_scaffold_6-snap.2594-T1
Valid prediction for Augustus_model.g10736.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_6-snap.2581-T1
Valid prediction for snap_scaffold_6-snap.2577-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.2605-T1
Valid prediction for GlimmerHMM_glimmerT_15988-T1
Valid prediction for GlimmerHMM_glimmerT_15989-T1
Valid prediction for GlimmerHMM_glimmerT_15995-T1
Couldn't classify 5652, 5800
Sorry, prediction pasa_asmbl_48742.p1 fails validation.
(AGC)	 CT	5652-5800	GT	AAG
(GTA)	 AG	6012-6047	GT	GAG
(GAG)	 AG	6292-6454	GT	GGG
(CCC)	 AG	7265-7381	TT	AAT
-recovered pasa_asmbl_48742.p1, terminal, 7265, 7381
-recovered pasa_asmbl_48742.p1, internal, 6012, 6047
-recovered pasa_asmbl_48742.p1, internal, 6292, 6454
Valid prediction for GeneMark_model.26828_t
Valid prediction for GeneMark_model.26832_t
Valid prediction for Augustus_model.g10749.t1
Valid prediction for CodingQuarry_transcript_55101-T1
Valid prediction for Augustus_model.g10729.t1
Valid prediction for snap_scaffold_6-snap.2587-T1
Valid prediction for Augustus_model.g10747.t1
Valid prediction for snap_scaffold_6-snap.2598-T1
Valid prediction for GeneMark_model.26830_t
Valid prediction for Augustus_model.g10730.t1
Valid prediction for Augustus_model.g10737.t1
Valid prediction for snap_scaffold_6-snap.2585-T1
Valid prediction for Augustus_model.g10732.t1
Valid prediction for Augustus_model.g10746.t1
Valid prediction for snap_scaffold_6-snap.2575-T1
Valid prediction for GeneMark_model.26821_t
Valid prediction for GeneMark_model.26809_t
Valid prediction for GlimmerHMM_glimmerT_15990-T1
Valid prediction for GeneMark_model.26816_t
Valid prediction for snap_scaffold_6-snap.2592-T1
Valid prediction for GlimmerHMM_glimmerT_15992-T1
Valid prediction for GeneMark_model.26833_t
Valid prediction for GlimmerHMM_glimmerT_16007-T1
Valid prediction for snap_scaffold_6-snap.2600-T1
Valid prediction for snap_scaffold_6-snap.2602-T1
Valid prediction for Augustus_model.g10735.t1
Valid prediction for GeneMark_model.26810_t
Valid prediction for snap_scaffold_6-snap.2576-T1
Valid prediction for GlimmerHMM_glimmerT_16012-T1
Valid prediction for snap_scaffold_6-snap.2604-T1
Valid prediction for GlimmerHMM_glimmerT_16009-T1
Couldn't classify 30217, 30368
Sorry, prediction pasa_asmbl_48737.p1 fails validation.
(GAG)	 CA	30217-30368	GT	TGG
(GAA)	 AG	30663-30780	GT	TGG
(AAA)	 AG	31061-31237	AA	GAA
-recovered pasa_asmbl_48737.p1, terminal, 31061, 31237
-recovered pasa_asmbl_48737.p1, internal, 30663, 30780
Valid prediction for snap_scaffold_6-snap.2584-T1
Valid prediction for snap_scaffold_6-snap.2589-T1
Valid prediction for snap_scaffold_6-snap.2580-T1
Valid prediction for GeneMark_model.26814_t
Valid prediction for snap_scaffold_6-snap.2603-T1
Valid prediction for GeneMark_model.26811_t
Valid prediction for GeneMark_model.26825_t
Valid prediction for GlimmerHMM_glimmerT_15997-T1
Valid prediction for GeneMark_model.26822_t
Valid prediction for Augustus_model.g10744.t1
Valid prediction for Augustus_model.g10740.t1
Valid prediction for GlimmerHMM_glimmerT_16003-T1

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

-building trellis in range 1 - 165769
-exon list size: 324


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.5    
2.8    
3.1    
3.4    
3.7    
4.0    
4.3    
4.6    
4.9    
5.2    
5.5    
5.8    
6.1    
6.4    
6.7    
7.1    
7.4    
7.7    
8.0    
8.3    
8.6    
8.9    
9.2    
9.5    
9.8    
10.1    
10.4    
10.7    
11.0    
11.3    
11.7    
12.0    
12.3    
12.6    
12.9    
13.2    
13.5    
13.8    
14.1    
14.4    
14.7    
15.0    
15.3    
15.6    
16.0    
16.3    
16.6    
16.9    
17.2    
17.5    
17.8    
18.1    
18.4    
18.7    
19.0    
19.3    
19.6    
19.9    
20.2    
20.6    
20.9    
21.2    
21.5    
21.8    
22.1    
22.4    
22.7    
23.0    
23.3    
23.6    
23.9    
24.2    
24.5    
24.8    
25.2    
25.5    
25.8    
26.1    
26.4    
26.7    
27.0    
27.3    
27.6    
27.9    
28.2    
28.5    
28.8    
29.1    
29.4    
29.8    
30.1    
30.4    
30.7    
31.0    
31.3    
31.6    
31.9    
32.2    
32.5    
32.8    
33.1    
33.4    
33.7    
34.0    
34.4    
34.7    
35.0    
35.3    
35.6    
35.9    
36.2    
36.5    
36.8    
37.1    
37.4    
37.7    
38.0    
38.3    
38.7    
39.0    
39.3    
39.6    
39.9    
40.2    
40.5    
40.8    
41.1    
41.4    
41.7    
42.0    
42.3    
42.6    
42.9    
43.3    
43.6    
43.9    
44.2    
44.5    
44.8    
45.1    
45.4    
45.7    
46.0    
46.3    
46.6    
46.9    
47.2    
47.5    
47.9    
48.2    
48.5    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.5    
51.8    
52.1    
52.5    
52.8    
53.1    
53.4    
53.7    
54.0    
54.3    
54.6    
54.9    
55.2    
55.5    
55.8    
56.1    
56.4    
56.7    
57.1    
57.4    
57.7    
58.0    
58.3    
58.6    
58.9    
59.2    
59.5    
59.8    
60.1    
60.4    
60.7    
61.0    
61.3    
61.7    
62.0    
62.3    
62.6    
62.9    
63.2    
63.5    
63.8    
64.1    
64.4    
64.7    
65.0    
65.3    
65.6    
66.0    
66.3    
66.6    
66.9    
67.2    
67.5    
67.8    
68.1    
68.4    
68.7    
69.0    
69.3    
69.6    
69.9    
70.2    
70.6    
70.9    
71.2    
71.5    
71.8    
72.1    
72.4    
72.7    
73.0    
73.3    
73.6    
73.9    
74.2    
74.5    
74.8    
75.2    
75.5    
75.8    
76.1    
76.4    
76.7    
77.0    
77.3    
77.6    
77.9    
78.2    
78.5    
78.8    
79.1    
79.4    
79.8    
80.1    
80.4    
80.7    
81.0    
81.3    
81.6    
81.9    
82.2    
82.5    
82.8    
83.1    
83.4    
83.7    
84.0    
84.4    
84.7    
85.0    
85.3    
85.6    
85.9    
86.2    
86.5    
86.8    
87.1    
87.4    
87.7    
88.0    
88.3    
88.7    
89.0    
89.3    
89.6    
89.9    
90.2    
90.5    
90.8    
91.1    
91.4    
91.7    
92.0    
92.3    
92.6    
92.9    
93.3    
93.6    
93.9    
94.2    
94.5    
94.8    
95.1    
95.4    
95.7    
96.0    
96.3    
96.6    
96.9    
97.2    
97.5    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 28 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support