-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_13550102-13748419

-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_7604-T1
Valid prediction for GlimmerHMM_glimmerT_7612-T1
Valid prediction for snap_scaffold_3-snap.2609-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_7633-T1
Valid prediction for snap_scaffold_3-snap.2629-T1
Valid prediction for Augustus_model.g4982.t1
Valid prediction for GlimmerHMM_glimmerT_7630-T1
Valid prediction for Augustus_model.g4993.t1
Valid prediction for Augustus_model.g4986.t1
Valid prediction for snap_scaffold_3-snap.2619-T1
Valid prediction for snap_scaffold_3-snap.2622-T1
Valid prediction for snap_scaffold_3-snap.2617-T1
Valid prediction for Augustus_model.g5002.t1
Valid prediction for Augustus_model.g4980.t1
Valid prediction for Augustus_model.g4984.t1
Valid prediction for GlimmerHMM_glimmerT_7627-T1
Valid prediction for snap_scaffold_3-snap.2607-T1
Valid prediction for GlimmerHMM_glimmerT_7609-T1
Valid prediction for snap_scaffold_3-snap.2615-T1
Valid prediction for CodingQuarry_transcript_46329-T1
Couldn't classify 67586, 67732
Couldn't classify 68906, 68987
Sorry, prediction pasa_asmbl_40815.p1 fails validation.
(GGG)	 CA	67586-67732	GT	AGG
(ATT)	 AG	68204-68290	GT	AGG
(AGC)	 AG	68383-68441	GT	AGG
(ACT)	 AG	68906-68987	GT	AGG
add_exon() Sorry, pasa_asmbl_40815.p1 68383-68441-terminal-2 is invalid.
-recovered pasa_asmbl_40815.p1, terminal, 68383, 68441
-recovered pasa_asmbl_40815.p1, internal, 68204, 68290
-recovered pasa_asmbl_40815.p1, internal, 68383, 68441
-recovered pasa_asmbl_40815.p1, internal, 68906, 68987
Valid prediction for snap_scaffold_3-snap.2603-T1
Valid prediction for pasa_asmbl_40450.p1
Valid prediction for snap_scaffold_3-snap.2606-T1
Valid prediction for snap_scaffold_3-snap.2627-T1
Valid prediction for GlimmerHMM_glimmerT_7621-T1
Valid prediction for HiQ_model.g5001.t1
Valid prediction for Augustus_model.g4978.t1
Valid prediction for Augustus_model.g4976.t1
Valid prediction for snap_scaffold_3-snap.2608-T1
Valid prediction for CodingQuarry_transcript_46328-T1
Valid prediction for snap_scaffold_3-snap.2605-T1
Valid prediction for snap_scaffold_3-snap.2618-T1
Valid prediction for GlimmerHMM_glimmerT_7606-T1
Valid prediction for snap_scaffold_3-snap.2628-T1
Valid prediction for snap_scaffold_3-snap.2623-T1
Valid prediction for Augustus_model.g4996.t1
Valid prediction for GlimmerHMM_glimmerT_7615-T1
Valid prediction for Augustus_model.g4999.t1
Valid prediction for Augustus_model.g4987.t1
Valid prediction for GlimmerHMM_glimmerT_7624-T1
Valid prediction for GlimmerHMM_glimmerT_7607-T1
Valid prediction for GlimmerHMM_glimmerT_7631-T1
Valid prediction for GlimmerHMM_glimmerT_7614-T1
Valid prediction for GlimmerHMM_glimmerT_7626-T1
Valid prediction for Augustus_model.g5000.t1
Couldn't classify 24764, 25066
Sorry, prediction pasa_asmbl_40855.p1 fails validation.
(TTT)	 TG	24764-25066	CC	GCC
Valid prediction for GlimmerHMM_glimmerT_7632-T1
Valid prediction for GlimmerHMM_glimmerT_7625-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_3-snap.2616-T1
Valid prediction for snap_scaffold_3-snap.2621-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.2612-T1
Valid prediction for GlimmerHMM_glimmerT_7634-T1
Valid prediction for Augustus_model.g4981.t1
Valid prediction for snap_scaffold_3-snap.2624-T1
Valid prediction for Augustus_model.g4983.t1
Valid prediction for pasa_asmbl_39293.p1
Valid prediction for Augustus_model.g4992.t1
Valid prediction for snap_scaffold_3-snap.2610-T1
Valid prediction for GlimmerHMM_glimmerT_7636-T1
Valid prediction for snap_scaffold_3-snap.2633-T1
Valid prediction for GlimmerHMM_glimmerT_7623-T1
Valid prediction for Augustus_model.g4979.t1
Valid prediction for GlimmerHMM_glimmerT_7610-T1
Valid prediction for HiQ_model.g4995.t1
Valid prediction for CodingQuarry_transcript_46331-T1
Valid prediction for GlimmerHMM_glimmerT_7620-T1
Valid prediction for snap_scaffold_3-snap.2604-T1
Valid prediction for Augustus_model.g4997.t1
Valid prediction for Augustus_model.g4989.t1
Valid prediction for HiQ_model.g5003.t1
Couldn't classify 82433, 82507
Couldn't classify 84068, 84132
Sorry, prediction pasa_asmbl_39280.p1 fails validation.
(CAT)	 AG	82433-82507	GT	AGG
(AGC)	 AG	83482-83610	GT	CGG
(GGA)	 AG	83742-83832	GT	AGG
(CTC)	 AG	84068-84132	AT	GTA
-recovered pasa_asmbl_39280.p1, internal, 82433, 82507
-recovered pasa_asmbl_39280.p1, internal, 83482, 83610
-recovered pasa_asmbl_39280.p1, internal, 83742, 83832
Valid prediction for GlimmerHMM_glimmerT_7628-T1
Valid prediction for Augustus_model.g4977.t1
Valid prediction for GlimmerHMM_glimmerT_7629-T1
Valid prediction for snap_scaffold_3-snap.2625-T1
Valid prediction for CodingQuarry_transcript_46330-T1
Valid prediction for GlimmerHMM_glimmerT_7618-T1
Valid prediction for GlimmerHMM_glimmerT_7613-T1
Valid prediction for Augustus_model.g4990.t1
Valid prediction for snap_scaffold_3-snap.2613-T1
Valid prediction for GlimmerHMM_glimmerT_7617-T1
Valid prediction for Augustus_model.g5004.t1
Valid prediction for Augustus_model.g4985.t1
Valid prediction for GlimmerHMM_glimmerT_7605-T1
Valid prediction for snap_scaffold_3-snap.2632-T1
Valid prediction for Augustus_model.g4998.t1
Valid prediction for GlimmerHMM_glimmerT_7619-T1
Valid prediction for GlimmerHMM_glimmerT_7611-T1
Valid prediction for Augustus_model.g4991.t1
Valid prediction for GlimmerHMM_glimmerT_7616-T1
Valid prediction for GlimmerHMM_glimmerT_7622-T1
Valid prediction for Augustus_model.g4994.t1
Valid prediction for GlimmerHMM_glimmerT_7637-T1
Valid prediction for snap_scaffold_3-snap.2614-T1
Valid prediction for snap_scaffold_3-snap.2634-T1
Valid prediction for snap_scaffold_3-snap.2630-T1
Valid prediction for GlimmerHMM_glimmerT_7608-T1
Couldn't classify 71028, 71127
Sorry, prediction pasa_asmbl_39285.p1 fails validation.
(AGT)	 AG	71028-71127	GT	TGG
(AGA)	 AG	71478-71556	GT	AGG
(TGG)	 AG	72702-72837	GT	AGG
(GTT)	 AG	72924-73004	GG	GAG
-recovered pasa_asmbl_39285.p1, terminal, 72924, 73004
-recovered pasa_asmbl_39285.p1, internal, 71028, 71127
-recovered pasa_asmbl_39285.p1, internal, 71478, 71556
-recovered pasa_asmbl_39285.p1, internal, 72702, 72837
Valid prediction for snap_scaffold_3-snap.2631-T1
Valid prediction for snap_scaffold_3-snap.2626-T1
Valid prediction for snap_scaffold_3-snap.2620-T1
Valid prediction for snap_scaffold_3-snap.2611-T1
Valid prediction for Augustus_model.g4988.t1
Valid prediction for GlimmerHMM_glimmerT_7635-T1

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

-building trellis in range 1 - 198318
-exon list size: 270


building trellis

0.4    
0.7    
1.1    
1.5    
1.8    
2.2    
2.6    
2.9    
3.3    
3.7    
4.0    
4.4    
4.8    
5.1    
5.5    
5.9    
6.2    
6.6    
7.0    
7.4    
7.7    
8.1    
8.5    
8.8    
9.2    
9.6    
9.9    
10.3    
10.7    
11.0    
11.4    
11.8    
12.1    
12.5    
12.9    
13.2    
13.6    
14.0    
14.3    
14.7    
15.1    
15.4    
15.8    
16.2    
16.5    
16.9    
17.3    
17.6    
18.0    
18.4    
18.8    
19.1    
19.5    
19.9    
20.2    
20.6    
21.0    
21.3    
21.7    
22.1    
22.4    
22.8    
23.2    
23.5    
23.9    
24.3    
24.6    
25.0    
25.4    
25.7    
26.1    
26.5    
26.8    
27.2    
27.6    
27.9    
28.3    
28.7    
29.0    
29.4    
29.8    
30.1    
30.5    
30.9    
31.2    
31.6    
32.0    
32.4    
32.7    
33.1    
33.5    
33.8    
34.2    
34.6    
34.9    
35.3    
35.7    
36.0    
36.4    
36.8    
37.1    
37.5    
37.9    
38.2    
38.6    
39.0    
39.3    
39.7    
40.1    
40.4    
40.8    
41.2    
41.5    
41.9    
42.3    
42.6    
43.0    
43.4    
43.8    
44.1    
44.5    
44.9    
45.2    
45.6    
46.0    
46.3    
46.7    
47.1    
47.4    
47.8    
48.2    
48.5    
48.9    
49.3    
49.6    
50.0    
50.4    
50.7    
51.1    
51.5    
51.8    
52.2    
52.6    
52.9    
53.3    
53.7    
54.0    
54.4    
54.8    
55.1    
55.5    
55.9    
56.2    
56.6    
57.0    
57.4    
57.7    
58.1    
58.5    
58.8    
59.2    
59.6    
59.9    
60.3    
60.7    
61.0    
61.4    
61.8    
62.1    
62.5    
62.9    
63.2    
63.6    
64.0    
64.3    
64.7    
65.1    
65.4    
65.8    
66.2    
66.5    
66.9    
67.3    
67.6    
68.0    
68.4    
68.8    
69.1    
69.5    
69.9    
70.2    
70.6    
71.0    
71.3    
71.7    
72.1    
72.4    
72.8    
73.2    
73.5    
73.9    
74.3    
74.6    
75.0    
75.4    
75.7    
76.1    
76.5    
76.8    
77.2    
77.6    
77.9    
78.3    
78.7    
79.0    
79.4    
79.8    
80.1    
80.5    
80.9    
81.2    
81.6    
82.0    
82.4    
82.7    
83.1    
83.5    
83.8    
84.2    
84.6    
84.9    
85.3    
85.7    
86.0    
86.4    
86.8    
87.1    
87.5    
87.9    
88.2    
88.6    
89.0    
89.3    
89.7    
90.1    
90.4    
90.8    
91.2    
91.5    
91.9    
92.3    
92.6    
93.0    
93.4    
93.8    
94.1    
94.5    
94.9    
95.2    
95.6    
96.0    
96.3    
96.7    
97.1    
97.4    
97.8    
98.2    
98.5    
98.9    
99.3    
99.6    
-found 33 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 32 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 185003 - 198318
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 185099 - 198318
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 186444 - 198318
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal

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