-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_11393192-11711863

-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 Augustus_model.g10338.t1
Valid prediction for GlimmerHMM_glimmerT_15515-T1
Valid prediction for HiQ_model.g10355.t1
Valid prediction for snap_scaffold_6-snap.2439-T1
Valid prediction for snap_scaffold_6-snap.2456-T1
Valid prediction for Augustus_model.g10350.t1
Valid prediction for HiQ_model.g10340.t1
Valid prediction for CodingQuarry_transcript_55229-T1
Valid prediction for snap_scaffold_6-snap.2457-T1
Valid prediction for Augustus_model.g10363.t1
Valid prediction for GlimmerHMM_glimmerT_15511-T1
Valid prediction for CodingQuarry_transcript_55236-T1
Valid prediction for pasa_asmbl_47325.p1
Valid prediction for snap_scaffold_6-snap.2461-T1
Valid prediction for GlimmerHMM_glimmerT_15532-T1
Valid prediction for snap_scaffold_6-snap.2468-T1
Valid prediction for GlimmerHMM_glimmerT_15521-T1
Valid prediction for GlimmerHMM_glimmerT_15512-T1
Valid prediction for snap_scaffold_6-snap.2463-T1
Valid prediction for GlimmerHMM_glimmerT_15529-T1
Valid prediction for snap_scaffold_6-snap.2443-T1
Couldn't classify 121022, 121022
Sorry, prediction CodingQuarry_transcript_55232-T1 fails validation.
(AGT)	 TC	121022-121022	GT	CAG
(TGA)	 AG	123412-123596	GT	GAG
-recovered CodingQuarry_transcript_55232-T1, terminal, 123412, 123596
-recovered CodingQuarry_transcript_55232-T1, internal, 123412, 123596
Valid prediction for GlimmerHMM_glimmerT_15514-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.2442-T1
Valid prediction for snap_scaffold_6-snap.2430-T1
Valid prediction for snap_scaffold_6-snap.2437-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.2472-T1
Valid prediction for CodingQuarry_transcript_55224-T1
Couldn't classify 202104, 202119
Couldn't classify 205940, 206008
Sorry, prediction pasa_asmbl_47353.p1 fails validation.
(GGT)	 AG	202104-202119	GT	GGG
(GTA)	 AG	203409-203466	GT	AAG
(AAA)	 AG	203579-203731	GT	AAG
(AGT)	 AG	203848-203899	GT	AGG
(AGT)	 AG	205940-206008	AA	GGA
add_exon() Sorry, pasa_asmbl_47353.p1 203409-203466-terminal-3 is invalid.
-recovered pasa_asmbl_47353.p1, terminal, 203409, 203466
-recovered pasa_asmbl_47353.p1, internal, 202104, 202119
-recovered pasa_asmbl_47353.p1, internal, 203409, 203466
-recovered pasa_asmbl_47353.p1, internal, 203579, 203731
-recovered pasa_asmbl_47353.p1, internal, 203848, 203899
Valid prediction for snap_scaffold_6-snap.2471-T1
Valid prediction for snap_scaffold_6-snap.2448-T1
Valid prediction for GlimmerHMM_glimmerT_15522-T1
Valid prediction for snap_scaffold_6-snap.2477-T1
Valid prediction for snap_scaffold_6-snap.2431-T1
Valid prediction for HiQ_model.g10342.t1
Valid prediction for GlimmerHMM_glimmerT_15525-T1
Valid prediction for Augustus_model.g10346.t1
Valid prediction for snap_scaffold_6-snap.2467-T1
Valid prediction for GlimmerHMM_glimmerT_15528-T1
Valid prediction for CodingQuarry_transcript_55231-T1
Valid prediction for snap_scaffold_6-snap.2454-T1
Valid prediction for Augustus_model.g10354.t1
Valid prediction for snap_scaffold_6-snap.2429-T1
Valid prediction for GlimmerHMM_glimmerT_15524-T1
Valid prediction for GlimmerHMM_glimmerT_15540-T1
Valid prediction for snap_scaffold_6-snap.2441-T1
Valid prediction for GlimmerHMM_glimmerT_15519-T1
Valid prediction for pasa_asmbl_47322.p1
Valid prediction for CodingQuarry_transcript_55233-T1
Valid prediction for snap_scaffold_6-snap.2447-T1
Valid prediction for Augustus_model.g10357.t1
Valid prediction for Augustus_model.g10345.t1
Valid prediction for pasa_asmbl_47352.p1
Valid prediction for snap_scaffold_6-snap.2464-T1
Valid prediction for Augustus_model.g10356.t1
Valid prediction for snap_scaffold_6-snap.2438-T1
Valid prediction for Augustus_model.g10331.t1
Valid prediction for snap_scaffold_6-snap.2466-T1
Valid prediction for snap_scaffold_6-snap.2462-T1
Valid prediction for GlimmerHMM_glimmerT_15509-T1
Valid prediction for HiQ_model.g10334.t1
Valid prediction for GlimmerHMM_glimmerT_15518-T1
Valid prediction for CodingQuarry_transcript_55228-T1
Valid prediction for CodingQuarry_transcript_55230-T1
Valid prediction for Augustus_model.g10332.t1
Valid prediction for GlimmerHMM_glimmerT_15535-T1
Valid prediction for GlimmerHMM_glimmerT_15516-T1
Valid prediction for snap_scaffold_6-snap.2440-T1
Valid prediction for snap_scaffold_6-snap.2434-T1
Valid prediction for Augustus_model.g10344.t1
Couldn't classify 73009, 73325
Couldn't classify 73889, 73932
Sorry, prediction pasa_asmbl_47323.p1 fails validation.
(GGA)	 CT	73009-73325	GT	TGG
(TGA)	 AG	73417-73643	GT	AGG
(ATG)	 AG	73889-73932	AA	CGA
-recovered pasa_asmbl_47323.p1, internal, 73417, 73643
Valid prediction for snap_scaffold_6-snap.2453-T1
Valid prediction for GlimmerHMM_glimmerT_15536-T1
Valid prediction for snap_scaffold_6-snap.2450-T1
Valid prediction for snap_scaffold_6-snap.2449-T1
Valid prediction for snap_scaffold_6-snap.2452-T1
Valid prediction for GlimmerHMM_glimmerT_15541-T1
Valid prediction for snap_scaffold_6-snap.2469-T1
Valid prediction for GlimmerHMM_glimmerT_15517-T1
Valid prediction for Augustus_model.g10362.t1
Valid prediction for snap_scaffold_6-snap.2473-T1
Valid prediction for Augustus_model.g10365.t1
Valid prediction for pasa_asmbl_47326.p1
Valid prediction for Augustus_model.g10336.t1
Couldn't classify 168671, 168886
Sorry, prediction pasa_asmbl_47348.p1 fails validation.
(ATG)	 TT	167800-168009	GT	AAG
(GTG)	 AG	168182-168496	GT	AGG
(GTG)	 AG	168671-168886	GC	CAG
-recovered pasa_asmbl_47348.p1, initial, 167800, 168009
-recovered pasa_asmbl_47348.p1, internal, 168182, 168496
-recovered pasa_asmbl_47348.p1, internal, 168671, 168886
Valid prediction for CodingQuarry_transcript_55227-T1
Valid prediction for snap_scaffold_6-snap.2451-T1
Valid prediction for pasa_asmbl_47335.p1
Valid prediction for HiQ_model.g10341.t1
Valid prediction for Augustus_model.g10347.t1
Valid prediction for pasa_asmbl_47336.p1
Valid prediction for snap_scaffold_6-snap.2435-T1
Valid prediction for Augustus_model.g10360.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 Augustus_model.g10353.t1
Valid prediction for snap_scaffold_6-snap.2465-T1
Valid prediction for Augustus_model.g10358.t1
Valid prediction for snap_scaffold_6-snap.2433-T1
Valid prediction for CodingQuarry_transcript_55234-T1
Valid prediction for GlimmerHMM_glimmerT_15526-T1
Valid prediction for snap_scaffold_6-snap.2446-T1
Valid prediction for pasa_asmbl_48759.p1
Valid prediction for Augustus_model.g10343.t1
Valid prediction for Augustus_model.g10333.t1
Valid prediction for snap_scaffold_6-snap.2459-T1
Valid prediction for GlimmerHMM_glimmerT_15520-T1
Valid prediction for pasa_asmbl_48755.p1
Couldn't classify 145980, 146172
Sorry, prediction pasa_asmbl_48766.p1 fails validation.
(TTC)	 TC	145980-146172	GT	AGG
(ATA)	 AG	146436-146530	GT	AGG
(TCT)	 AG	146716-146766	GT	AGG
(AAA)	 AG	146861-146965	GT	AGG
(GTT)	 AG	147183-147236	AT	GAA
-recovered pasa_asmbl_48766.p1, terminal, 147183, 147236
-recovered pasa_asmbl_48766.p1, internal, 146436, 146530
-recovered pasa_asmbl_48766.p1, internal, 146716, 146766
-recovered pasa_asmbl_48766.p1, internal, 146861, 146965
Valid prediction for snap_scaffold_6-snap.2445-T1
Valid prediction for Augustus_model.g10359.t1
Valid prediction for snap_scaffold_6-snap.2476-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for HiQ_model.g10335.t1
Valid prediction for snap_scaffold_6-snap.2436-T1
Valid prediction for Augustus_model.g10339.t1
Valid prediction for GlimmerHMM_glimmerT_15538-T1
Valid prediction for snap_scaffold_6-snap.2432-T1
Valid prediction for GlimmerHMM_glimmerT_15530-T1
Valid prediction for Augustus_model.g10352.t1
Valid prediction for snap_scaffold_6-snap.2478-T1
Valid prediction for snap_scaffold_6-snap.2455-T1
Valid prediction for pasa_asmbl_48758.p1
Valid prediction for GlimmerHMM_glimmerT_15510-T1
Valid prediction for GlimmerHMM_glimmerT_15539-T1
Valid prediction for GlimmerHMM_glimmerT_15527-T1
Valid prediction for Augustus_model.g10337.t1
Valid prediction for CodingQuarry_transcript_55225-T1
Valid prediction for snap_scaffold_6-snap.2470-T1
Valid prediction for snap_scaffold_6-snap.2444-T1
Valid prediction for GlimmerHMM_glimmerT_15542-T1
Valid prediction for HiQ_model.g10349.t1
Valid prediction for Augustus_model.g10361.t1
Valid prediction for GlimmerHMM_glimmerT_15537-T1
Valid prediction for Augustus_model.g10348.t1
Valid prediction for GlimmerHMM_glimmerT_15513-T1
Valid prediction for CodingQuarry_transcript_55235-T1
Valid prediction for Augustus_model.g10366.t1
Valid prediction for GlimmerHMM_glimmerT_15531-T1
Valid prediction for pasa_asmbl_48760.p1
Valid prediction for snap_scaffold_6-snap.2458-T1
Valid prediction for GlimmerHMM_glimmerT_15523-T1
Valid prediction for snap_scaffold_6-snap.2475-T1
Valid prediction for snap_scaffold_6-snap.2460-T1
Valid prediction for Augustus_model.g10364.t1
Valid prediction for GlimmerHMM_glimmerT_15533-T1
Valid prediction for snap_scaffold_6-snap.2474-T1
Valid prediction for GlimmerHMM_glimmerT_15534-T1
Valid prediction for CodingQuarry_transcript_55226-T1
Valid prediction for HiQ_model.g10351.t1

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

-building trellis in range 1 - 318672
-exon list size: 414


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
1.4    
1.7    
1.9    
2.2    
2.4    
2.6    
2.9    
3.1    
3.4    
3.6    
3.8    
4.1    
4.3    
4.6    
4.8    
5.0    
5.3    
5.5    
5.8    
6.0    
6.2    
6.5    
6.7    
7.0    
7.2    
7.5    
7.7    
7.9    
8.2    
8.4    
8.7    
8.9    
9.1    
9.4    
9.6    
9.9    
10.1    
10.3    
10.6    
10.8    
11.1    
11.3    
11.5    
11.8    
12.0    
12.3    
12.5    
12.7    
13.0    
13.2    
13.5    
13.7    
13.9    
14.2    
14.4    
14.7    
14.9    
15.1    
15.4    
15.6    
15.9    
16.1    
16.3    
16.6    
16.8    
17.1    
17.3    
17.5    
17.8    
18.0    
18.3    
18.5    
18.8    
19.0    
19.2    
19.5    
19.7    
20.0    
20.2    
20.4    
20.7    
20.9    
21.2    
21.4    
21.6    
21.9    
22.1    
22.4    
22.6    
22.8    
23.1    
23.3    
23.6    
23.8    
24.0    
24.3    
24.5    
24.8    
25.0    
25.2    
25.5    
25.7    
26.0    
26.2    
26.4    
26.7    
26.9    
27.2    
27.4    
27.6    
27.9    
28.1    
28.4    
28.6    
28.8    
29.1    
29.3    
29.6    
29.8    
30.0    
30.3    
30.5    
30.8    
31.0    
31.2    
31.5    
31.7    
32.0    
32.2    
32.5    
32.7    
32.9    
33.2    
33.4    
33.7    
33.9    
34.1    
34.4    
34.6    
34.9    
35.1    
35.3    
35.6    
35.8    
36.1    
36.3    
36.5    
36.8    
37.0    
37.3    
37.5    
37.7    
38.0    
38.2    
38.5    
38.7    
38.9    
39.2    
39.4    
39.7    
39.9    
40.1    
40.4    
40.6    
40.9    
41.1    
41.3    
41.6    
41.8    
42.1    
42.3    
42.5    
42.8    
43.0    
43.3    
43.5    
43.8    
44.0    
44.2    
44.5    
44.7    
45.0    
45.2    
45.4    
45.7    
45.9    
46.2    
46.4    
46.6    
46.9    
47.1    
47.4    
47.6    
47.8    
48.1    
48.3    
48.6    
48.8    
49.0    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
51.0    
51.2    
51.4    
51.7    
51.9    
52.2    
52.4    
52.6    
52.9    
53.1    
53.4    
53.6    
53.8    
54.1    
54.3    
54.6    
54.8    
55.0    
55.3    
55.5    
55.8    
56.0    
56.2    
56.5    
56.7    
57.0    
57.2    
57.5    
57.7    
57.9    
58.2    
58.4    
58.7    
58.9    
59.1    
59.4    
59.6    
59.9    
60.1    
60.3    
60.6    
60.8    
61.1    
61.3    
61.5    
61.8    
62.0    
62.3    
62.5    
62.7    
63.0    
63.2    
63.5    
63.7    
63.9    
64.2    
64.4    
64.7    
64.9    
65.1    
65.4    
65.6    
65.9    
66.1    
66.3    
66.6    
66.8    
67.1    
67.3    
67.5    
67.8    
68.0    
68.3    
68.5    
68.8    
69.0    
69.2    
69.5    
69.7    
70.0    
70.2    
70.4    
70.7    
70.9    
71.2    
71.4    
71.6    
71.9    
72.1    
72.4    
72.6    
72.8    
73.1    
73.3    
73.6    
73.8    
74.0    
74.3    
74.5    
74.8    
75.0    
75.2    
75.5    
75.7    
76.0    
76.2    
76.4    
76.7    
76.9    
77.2    
77.4    
77.6    
77.9    
78.1    
78.4    
78.6    
78.8    
79.1    
79.3    
79.6    
79.8    
80.0    
80.3    
80.5    
80.8    
81.0    
81.2    
81.5    
81.7    
82.0    
82.2    
82.5    
82.7    
82.9    
83.2    
83.4    
83.7    
83.9    
84.1    
84.4    
84.6    
84.9    
85.1    
85.3    
85.6    
85.8    
86.1    
86.3    
86.5    
86.8    
87.0    
87.3    
87.5    
87.7    
88.0    
88.2    
88.5    
88.7    
88.9    
89.2    
89.4    
89.7    
89.9    
90.1    
90.4    
90.6    
90.9    
91.1    
91.3    
91.6    
91.8    
92.1    
92.3    
92.5    
92.8    
93.0    
93.3    
93.5    
93.8    
94.0    
94.2    
94.5    
94.7    
95.0    
95.2    
95.4    
95.7    
95.9    
96.2    
96.4    
96.6    
96.9    
97.1    
97.4    
97.6    
97.8    
98.1    
98.3    
98.6    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 46 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 45 predictions persist after filtering for low support