-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_7/scaffold_7_4317497-4586277

-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 pasa_asmbl_49744.p1
Valid prediction for Augustus_model.g11568.t1
Valid prediction for Augustus_model.g11558.t1
Couldn't classify 203657, 203842
Sorry, prediction pasa_asmbl_49739.p1 fails validation.
(ATG)	 CT	196578-196663	GT	AGG
(TTC)	 AG	197978-198035	GT	TGG
(GTG)	 AG	198176-198330	GT	TGG
(GTA)	 AG	198455-198541	GT	AAG
(GTG)	 AG	200087-200175	GT	GAG
(GGT)	 AG	200313-200363	GT	AAG
(TTC)	 AG	201287-201451	GT	TGG
(AGC)	 AG	201563-201724	GT	AGG
(ATG)	 AG	202025-202166	GT	AAG
(GTG)	 AG	202389-202588	GT	TGG
(CTA)	 AG	202776-202829	GT	AGG
(CTG)	 AG	203449-203576	GT	AGG
(AGC)	 AG	203657-203842	AA	GTA
-recovered pasa_asmbl_49739.p1, initial, 196578, 196663
add_exon() Sorry, pasa_asmbl_49739.p1 202025-202166-initial-1 is invalid.
-recovered pasa_asmbl_49739.p1, initial, 202025, 202166
add_exon() Sorry, pasa_asmbl_49739.p1 198455-198541-terminal-1 is invalid.
-recovered pasa_asmbl_49739.p1, terminal, 198455, 198541
-recovered pasa_asmbl_49739.p1, internal, 197978, 198035
-recovered pasa_asmbl_49739.p1, internal, 198176, 198330
-recovered pasa_asmbl_49739.p1, internal, 198455, 198541
-recovered pasa_asmbl_49739.p1, internal, 200087, 200175
-recovered pasa_asmbl_49739.p1, internal, 200313, 200363
-recovered pasa_asmbl_49739.p1, internal, 201287, 201451
-recovered pasa_asmbl_49739.p1, internal, 201563, 201724
-recovered pasa_asmbl_49739.p1, internal, 202025, 202166
-recovered pasa_asmbl_49739.p1, internal, 202389, 202588
-recovered pasa_asmbl_49739.p1, internal, 202776, 202829
-recovered pasa_asmbl_49739.p1, internal, 203449, 203576
Valid prediction for snap_scaffold_7-snap.996-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_7-snap.987-T1
Valid prediction for CodingQuarry_transcript_57492-T1
Valid prediction for snap_scaffold_7-snap.1016-T1
Couldn't classify 210253, 210428
Couldn't classify 210533, 210653
Sorry, prediction pasa_asmbl_50579.p1 fails validation.
(GGT)	 CA	210253-210428	GT	AAG
(GTT)	 AG	210533-210653	AG	TCA
Valid prediction for snap_scaffold_7-snap.1015-T1
Valid prediction for GlimmerHMM_glimmerT_17308-T1
Valid prediction for Augustus_model.g11569.t1
Valid prediction for GlimmerHMM_glimmerT_17298-T1
Valid prediction for GlimmerHMM_glimmerT_17287-T1
Valid prediction for snap_scaffold_7-snap.1010-T1
Valid prediction for snap_scaffold_7-snap.1002-T1
Valid prediction for Augustus_model.g11553.t1
Valid prediction for snap_scaffold_7-snap.1007-T1
Valid prediction for Augustus_model.g11566.t1
Valid prediction for CodingQuarry_transcript_57490-T1
Valid prediction for snap_scaffold_7-snap.1003-T1
Valid prediction for Augustus_model.g11551.t1
Valid prediction for snap_scaffold_7-snap.1014-T1
Valid prediction for pasa_asmbl_49733.p1
Couldn't classify 213814, 213999
Couldn't classify 216050, 216155
Sorry, prediction pasa_asmbl_49741.p1 fails validation.
(ACT)	 CA	213814-213999	GT	AGG
(GTG)	 AG	214147-214273	GT	AGG
(GCC)	 AG	214365-214543	GT	AGG
(GTC)	 AG	214644-214758	GT	AGG
(GTG)	 AG	215737-215899	GT	ATG
(CTC)	 AG	216050-216155	GG	AAG
-recovered pasa_asmbl_49741.p1, internal, 214147, 214273
-recovered pasa_asmbl_49741.p1, internal, 214365, 214543
-recovered pasa_asmbl_49741.p1, internal, 214644, 214758
-recovered pasa_asmbl_49741.p1, internal, 215737, 215899
Valid prediction for snap_scaffold_7-snap.1006-T1
Valid prediction for GlimmerHMM_glimmerT_17310-T1
Valid prediction for GlimmerHMM_glimmerT_17304-T1
Valid prediction for snap_scaffold_7-snap.1011-T1
Valid prediction for GlimmerHMM_glimmerT_17307-T1
Valid prediction for HiQ_model.g11565.t1
Valid prediction for GlimmerHMM_glimmerT_17303-T1
Valid prediction for GlimmerHMM_glimmerT_17286-T1
Valid prediction for Augustus_model.g11556.t1
Valid prediction for snap_scaffold_7-snap.1012-T1
Valid prediction for snap_scaffold_7-snap.1009-T1
Valid prediction for Augustus_model.g11545.t1
Valid prediction for GlimmerHMM_glimmerT_17291-T1
Valid prediction for GlimmerHMM_glimmerT_17311-T1
Valid prediction for snap_scaffold_7-snap.984-T1
Valid prediction for snap_scaffold_7-snap.1013-T1
Valid prediction for Augustus_model.g11564.t1
Valid prediction for snap_scaffold_7-snap.1008-T1
Valid prediction for GlimmerHMM_glimmerT_17306-T1
Valid prediction for GlimmerHMM_glimmerT_17294-T1
Valid prediction for Augustus_model.g11559.t1
Couldn't classify 219411, 219462
Couldn't classify 222333, 222446
Sorry, prediction pasa_asmbl_50558.p1 fails validation.
(GTT)	 GT	219411-219462	GT	CAG
(TCA)	 AG	219837-219973	GT	ATG
(CCC)	 AG	220081-220225	GT	TGG
(CTT)	 AG	220342-220404	GT	GGG
(GCC)	 AG	220606-220673	GT	AGG
(GTG)	 AG	222333-222446	GT	AGG
-recovered pasa_asmbl_50558.p1, internal, 219837, 219973
-recovered pasa_asmbl_50558.p1, internal, 220081, 220225
-recovered pasa_asmbl_50558.p1, internal, 220342, 220404
-recovered pasa_asmbl_50558.p1, internal, 220606, 220673
-recovered pasa_asmbl_50558.p1, internal, 222333, 222446
Valid prediction for GlimmerHMM_glimmerT_17296-T1
Valid prediction for Augustus_model.g11555.t1
Valid prediction for Augustus_model.g11570.t1
Valid prediction for Augustus_model.g11563.t1
Valid prediction for GlimmerHMM_glimmerT_17289-T1
Valid prediction for GlimmerHMM_glimmerT_17305-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 GlimmerHMM_glimmerT_17290-T1
Valid prediction for Augustus_model.g11547.t1
Valid prediction for GlimmerHMM_glimmerT_17285-T1
Valid prediction for GlimmerHMM_glimmerT_17299-T1
Valid prediction for GlimmerHMM_glimmerT_17300-T1
Valid prediction for snap_scaffold_7-snap.999-T1
Valid prediction for snap_scaffold_7-snap.991-T1
Valid prediction for snap_scaffold_7-snap.995-T1
Valid prediction for Augustus_model.g11554.t1
Valid prediction for GlimmerHMM_glimmerT_17295-T1
Valid prediction for snap_scaffold_7-snap.1000-T1
Valid prediction for GlimmerHMM_glimmerT_17309-T1
Valid prediction for Augustus_model.g11561.t1
Valid prediction for Augustus_model.g11552.t1
Valid prediction for Augustus_model.g11550.t1
Valid prediction for GlimmerHMM_glimmerT_17302-T1
Valid prediction for Augustus_model.g11544.t1
Valid prediction for Augustus_model.g11567.t1
Valid prediction for Augustus_model.g11557.t1
Valid prediction for Augustus_model.g11549.t1
Valid prediction for GlimmerHMM_glimmerT_17297-T1
Valid prediction for GlimmerHMM_glimmerT_17283-T1
Valid prediction for snap_scaffold_7-snap.997-T1
Valid prediction for snap_scaffold_7-snap.1001-T1
Valid prediction for snap_scaffold_7-snap.986-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_57491-T1
Valid prediction for GlimmerHMM_glimmerT_17281-T1
Valid prediction for Augustus_model.g11548.t1
Valid prediction for snap_scaffold_7-snap.988-T1
Valid prediction for snap_scaffold_7-snap.989-T1
Valid prediction for snap_scaffold_7-snap.1004-T1
Valid prediction for snap_scaffold_7-snap.985-T1
Valid prediction for GlimmerHMM_glimmerT_17312-T1
Valid prediction for Augustus_model.g11560.t1
Valid prediction for snap_scaffold_7-snap.983-T1
Valid prediction for GlimmerHMM_glimmerT_17284-T1
Valid prediction for snap_scaffold_7-snap.994-T1
Valid prediction for snap_scaffold_7-snap.998-T1
Valid prediction for snap_scaffold_7-snap.1005-T1
Valid prediction for Augustus_model.g11543.t1
Valid prediction for Augustus_model.g11546.t1
Valid prediction for snap_scaffold_7-snap.990-T1
Valid prediction for HiQ_model.g11562.t1
Valid prediction for GlimmerHMM_glimmerT_17282-T1
Valid prediction for GlimmerHMM_glimmerT_17301-T1
Valid prediction for pasa_asmbl_50863.p1
Valid prediction for GlimmerHMM_glimmerT_17293-T1
Valid prediction for snap_scaffold_7-snap.992-T1
Valid prediction for GlimmerHMM_glimmerT_17292-T1
Valid prediction for snap_scaffold_7-snap.993-T1
Valid prediction for GlimmerHMM_glimmerT_17288-T1

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

-building trellis in range 1 - 268781
-exon list size: 319


building trellis

0.3    
0.6    
0.9    
1.2    
1.6    
1.9    
2.2    
2.5    
2.8    
3.1    
3.4    
3.7    
4.0    
4.4    
4.7    
5.0    
5.3    
5.6    
5.9    
6.2    
6.5    
6.9    
7.2    
7.5    
7.8    
8.1    
8.4    
8.7    
9.0    
9.3    
9.7    
10.0    
10.3    
10.6    
10.9    
11.2    
11.5    
11.8    
12.1    
12.5    
12.8    
13.1    
13.4    
13.7    
14.0    
14.3    
14.6    
15.0    
15.3    
15.6    
15.9    
16.2    
16.5    
16.8    
17.1    
17.4    
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    
23.1    
23.4    
23.7    
24.0    
24.3    
24.6    
24.9    
25.2    
25.5    
25.9    
26.2    
26.5    
26.8    
27.1    
27.4    
27.7    
28.0    
28.3    
28.7    
29.0    
29.3    
29.6    
29.9    
30.2    
30.5    
30.8    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
33.0    
33.3    
33.6    
34.0    
34.3    
34.6    
34.9    
35.2    
35.5    
35.8    
36.1    
36.4    
36.8    
37.1    
37.4    
37.7    
38.0    
38.3    
38.6    
38.9    
39.3    
39.6    
39.9    
40.2    
40.5    
40.8    
41.1    
41.4    
41.7    
42.1    
42.4    
42.7    
43.0    
43.3    
43.6    
43.9    
44.2    
44.5    
44.9    
45.2    
45.5    
45.8    
46.1    
46.4    
46.7    
47.0    
47.4    
47.7    
48.0    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
52.0    
52.3    
52.6    
53.0    
53.3    
53.6    
53.9    
54.2    
54.5    
54.8    
55.1    
55.5    
55.8    
56.1    
56.4    
56.7    
57.0    
57.3    
57.6    
57.9    
58.3    
58.6    
58.9    
59.2    
59.5    
59.8    
60.1    
60.4    
60.7    
61.1    
61.4    
61.7    
62.0    
62.3    
62.6    
62.9    
63.2    
63.6    
63.9    
64.2    
64.5    
64.8    
65.1    
65.4    
65.7    
66.0    
66.4    
66.7    
67.0    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.2    
69.5    
69.8    
70.1    
70.4    
70.7    
71.0    
71.3    
71.7    
72.0    
72.3    
72.6    
72.9    
73.2    
73.5    
73.8    
74.1    
74.5    
74.8    
75.1    
75.4    
75.7    
76.0    
76.3    
76.6    
76.9    
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    
82.6    
82.9    
83.2    
83.5    
83.8    
84.1    
84.4    
84.7    
85.0    
85.4    
85.7    
86.0    
86.3    
86.6    
86.9    
87.2    
87.5    
87.9    
88.2    
88.5    
88.8    
89.1    
89.4    
89.7    
90.0    
90.3    
90.7    
91.0    
91.3    
91.6    
91.9    
92.2    
92.5    
92.8    
93.1    
93.5    
93.8    
94.1    
94.4    
94.7    
95.0    
95.3    
95.6    
96.0    
96.3    
96.6    
96.9    
97.2    
97.5    
97.8    
98.1    
98.4    
98.8    
99.1    
99.4    
99.7    
-found 38 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 35 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 243428 - 268781
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 246351 - 268781
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 253639 - 268781
-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