-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_25/scaffold_25_9806345-10101399

-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.g36418.t1
Valid prediction for HiQ_model.g36406.t1
Valid prediction for GlimmerHMM_glimmerT_54849-T1
Valid prediction for GlimmerHMM_glimmerT_54861-T1
Valid prediction for snap_scaffold_25-snap.2093-T1
Valid prediction for GlimmerHMM_glimmerT_54864-T1
Valid prediction for snap_scaffold_25-snap.2104-T1
Valid prediction for snap_scaffold_25-snap.2109-T1
Valid prediction for snap_scaffold_25-snap.2107-T1
Valid prediction for GlimmerHMM_glimmerT_54851-T1
Valid prediction for Augustus_model.g36426.t1
Couldn't classify 111213, 111277
Couldn't classify 114907, 114960
Sorry, prediction pasa_asmbl_33849.p1 fails validation.
(AGA)	 TC	111213-111277	GT	TTG
(GGA)	 AG	111947-112032	GT	GGG
(TGG)	 AG	113923-114048	GT	CGG
(ATG)	 AG	114155-114249	GT	AGG
(GTA)	 AG	114907-114960	CA	CTC
add_exon() Sorry, pasa_asmbl_33849.p1 114155-114249-initial-1 is invalid.
-recovered pasa_asmbl_33849.p1, initial, 114155, 114249
-recovered pasa_asmbl_33849.p1, internal, 111947, 112032
-recovered pasa_asmbl_33849.p1, internal, 113923, 114048
-recovered pasa_asmbl_33849.p1, internal, 114155, 114249
Valid prediction for snap_scaffold_25-snap.2086-T1
Valid prediction for GlimmerHMM_glimmerT_54859-T1
Valid prediction for Augustus_model.g36405.t1
Valid prediction for Augustus_model.g36425.t1
Valid prediction for GlimmerHMM_glimmerT_54845-T1
Valid prediction for snap_scaffold_25-snap.2103-T1
Valid prediction for Augustus_model.g36408.t1
Valid prediction for snap_scaffold_25-snap.2091-T1
Valid prediction for GlimmerHMM_glimmerT_54862-T1
Valid prediction for pasa_asmbl_33847.p1
Couldn't classify 275114, 275299
Sorry, prediction pasa_asmbl_33858.p1 fails validation.
(ATG)	 AA	273413-273541	GT	AGG
(ACA)	 AG	275114-275299	GG	CTG
-recovered pasa_asmbl_33858.p1, initial, 273413, 273541
Valid prediction for snap_scaffold_25-snap.2106-T1
Valid prediction for GlimmerHMM_glimmerT_54843-T1
Valid prediction for snap_scaffold_25-snap.2095-T1
Valid prediction for snap_scaffold_25-snap.2092-T1
Valid prediction for Augustus_model.g36421.t1
Valid prediction for snap_scaffold_25-snap.2084-T1
Valid prediction for GlimmerHMM_glimmerT_54847-T1
Valid prediction for Augustus_model.g36403.t1
Valid prediction for GlimmerHMM_glimmerT_54858-T1
Valid prediction for snap_scaffold_25-snap.2108-T1
Valid prediction for snap_scaffold_25-snap.2114-T1
Valid prediction for snap_scaffold_25-snap.2101-T1
Valid prediction for GlimmerHMM_glimmerT_54866-T1
Valid prediction for Augustus_model.g36415.t1
Valid prediction for GlimmerHMM_glimmerT_54856-T1
Valid prediction for Augustus_model.g36402.t1
Couldn't classify 249312, 249416
Couldn't classify 251867, 252027
Sorry, prediction pasa_asmbl_33854.p1 fails validation.
(AAG)	 AG	249312-249416	GT	ATG
(ATG)	 AG	249537-249639	GT	AGG
(GTG)	 AG	251867-252027	GT	AGG
-recovered pasa_asmbl_33854.p1, initial, 249537, 249639
add_exon() Sorry, pasa_asmbl_33854.p1 249537-249639-terminal-3 is invalid.
-recovered pasa_asmbl_33854.p1, terminal, 249537, 249639
-recovered pasa_asmbl_33854.p1, internal, 249312, 249416
-recovered pasa_asmbl_33854.p1, internal, 249537, 249639
-recovered pasa_asmbl_33854.p1, internal, 251867, 252027
Couldn't classify 212278, 212778
Sorry, prediction pasa_asmbl_33852.p1 fails validation.
(TTT)	 TA	212278-212778	CA	GAC
Valid prediction for GlimmerHMM_glimmerT_54841-T1
Valid prediction for Augustus_model.g36409.t1
Couldn't classify 204636, 205352
Sorry, prediction pasa_asmbl_33851.p1 fails validation.
(AGC)	 TC	204636-205352	AG	AGA
Valid prediction for Augustus_model.g36414.t1
Valid prediction for GlimmerHMM_glimmerT_54844-T1
Valid prediction for Augustus_model.g36423.t1
Valid prediction for snap_scaffold_25-snap.2100-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_25-snap.2111-T1
Valid prediction for snap_scaffold_25-snap.2110-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_54860-T1
Valid prediction for snap_scaffold_25-snap.2089-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_25-snap.2085-T1
Valid prediction for Augustus_model.g36413.t1
Valid prediction for snap_scaffold_25-snap.2113-T1
Couldn't classify 148442, 148471
Couldn't classify 150824, 151016
Sorry, prediction pasa_asmbl_34598.p1 fails validation.
(CTT)	 AT	148442-148471	GT	TGG
(CAT)	 AG	148607-148717	GT	AGG
(AGA)	 AG	150601-150725	GT	TGG
(GGA)	 AG	150824-151016	TC	AGT
-recovered pasa_asmbl_34598.p1, internal, 148607, 148717
-recovered pasa_asmbl_34598.p1, internal, 150601, 150725
Couldn't classify 205264, 205611
Sorry, prediction pasa_asmbl_34547.p1 fails validation.
(AGA)	 TC	205264-205611	AC	ACA
Valid prediction for snap_scaffold_25-snap.2112-T1
Valid prediction for snap_scaffold_25-snap.2087-T1
Valid prediction for GlimmerHMM_glimmerT_54842-T1
Valid prediction for GlimmerHMM_glimmerT_54865-T1
Valid prediction for snap_scaffold_25-snap.2098-T1
Couldn't classify 219032, 219139
Couldn't classify 219352, 219567
Sorry, prediction pasa_asmbl_34556.p1 fails validation.
(AGC)	 AC	219032-219139	GT	ATG
(GTT)	 AG	219352-219567	GT	AGG
-recovered pasa_asmbl_34556.p1, internal, 219352, 219567
Valid prediction for GlimmerHMM_glimmerT_54868-T1
Valid prediction for snap_scaffold_25-snap.2102-T1
Valid prediction for CodingQuarry_transcript_38840-T1
Valid prediction for snap_scaffold_25-snap.2088-T1
Valid prediction for Augustus_model.g36422.t1
Valid prediction for Augustus_model.g36417.t1
Valid prediction for GlimmerHMM_glimmerT_54867-T1
Valid prediction for HiQ_model.g36419.t1
Valid prediction for Augustus_model.g36416.t1
Valid prediction for snap_scaffold_25-snap.2099-T1
Valid prediction for GlimmerHMM_glimmerT_54854-T1
Valid prediction for snap_scaffold_25-snap.2090-T1
Valid prediction for Augustus_model.g36412.t1
Valid prediction for CodingQuarry_transcript_38839-T1
Valid prediction for CodingQuarry_transcript_38841-T1
Valid prediction for GlimmerHMM_glimmerT_54863-T1
Valid prediction for HiQ_model.g36420.t1
Valid prediction for Augustus_model.g36404.t1
Valid prediction for snap_scaffold_25-snap.2116-T1
Valid prediction for pasa_asmbl_34528.p1
Couldn't classify 255191, 255523
Sorry, prediction pasa_asmbl_33846.p1 fails validation.
(AAA)	 CC	255191-255523	GG	GTG
Valid prediction for snap_scaffold_25-snap.2115-T1
Valid prediction for snap_scaffold_25-snap.2105-T1
Couldn't classify 225645, 225773
Couldn't classify 226425, 226598
Sorry, prediction pasa_asmbl_34525.p1 fails validation.
(GAG)	 CA	225645-225773	GT	AGG
(GGT)	 AG	225950-226168	GT	AGG
(GTG)	 AG	226425-226598	GG	CAG
-recovered pasa_asmbl_34525.p1, internal, 225950, 226168
Couldn't classify 211617, 211920
Sorry, prediction pasa_asmbl_34527.p1 fails validation.
(ATG)	 AC	209909-209964	GT	AGG
(CAC)	 AG	211617-211920	GA	TGG
-recovered pasa_asmbl_34527.p1, initial, 209909, 209964
Couldn't classify 57529, 57615
Couldn't classify 57963, 58060
Sorry, prediction pasa_asmbl_34537.p1 fails validation.
(CTC)	 CC	57529-57615	GT	AGG
(GGC)	 AG	57716-57869	GT	TGG
(GCA)	 AG	57963-58060	AG	AGA
-recovered pasa_asmbl_34537.p1, internal, 57716, 57869
Couldn't classify 154102, 154357
Sorry, prediction pasa_asmbl_34531.p1 fails validation.
(CAC)	 TT	154102-154357	GT	AGG
(AAT)	 AG	156733-156816	GT	AGG
(CGG)	 AG	156918-157000	GT	ATG
(GCC)	 AG	157090-157185	GT	GGG
(ATC)	 AG	159101-159206	GT	AGG
(GTC)	 AG	160781-160832	GT	AGG
(AAG)	 AG	162109-162197	GT	ATG
(GGT)	 AG	164221-164309	GT	AAG
(TTA)	 AG	166576-166692	GT	AGG
(AAT)	 AG	166782-166895	GT	AGG
(GTT)	 AG	167937-168024	GT	CCG
(GCA)	 AG	168575-168723	TT	GAT
-recovered pasa_asmbl_34531.p1, terminal, 168575, 168723
-recovered pasa_asmbl_34531.p1, internal, 156733, 156816
-recovered pasa_asmbl_34531.p1, internal, 156918, 157000
-recovered pasa_asmbl_34531.p1, internal, 157090, 157185
-recovered pasa_asmbl_34531.p1, internal, 159101, 159206
-recovered pasa_asmbl_34531.p1, internal, 160781, 160832
-recovered pasa_asmbl_34531.p1, internal, 162109, 162197
-recovered pasa_asmbl_34531.p1, internal, 164221, 164309
-recovered pasa_asmbl_34531.p1, internal, 166576, 166692
-recovered pasa_asmbl_34531.p1, internal, 166782, 166895
-recovered pasa_asmbl_34531.p1, internal, 167937, 168024
Couldn't classify 277068, 277133
Couldn't classify 280903, 280985
Sorry, prediction pasa_asmbl_34523.p1 fails validation.
(GCT)	 TG	277068-277133	GT	AGG
(AGG)	 AG	277747-277879	GT	AGG
(GTC)	 AG	279653-279814	GT	GGG
(ACG)	 AG	280085-280135	GT	AGG
(GAG)	 AG	280903-280985	AT	TGA
-recovered pasa_asmbl_34523.p1, internal, 277747, 277879
-recovered pasa_asmbl_34523.p1, internal, 279653, 279814
-recovered pasa_asmbl_34523.p1, internal, 280085, 280135
Valid prediction for GlimmerHMM_glimmerT_54846-T1
Valid prediction for GlimmerHMM_glimmerT_54848-T1
Valid prediction for GlimmerHMM_glimmerT_54850-T1
Valid prediction for GlimmerHMM_glimmerT_54857-T1
Valid prediction for Augustus_model.g36424.t1
Valid prediction for snap_scaffold_25-snap.2097-T1
Valid prediction for GlimmerHMM_glimmerT_54852-T1
Valid prediction for GlimmerHMM_glimmerT_54853-T1
Valid prediction for snap_scaffold_25-snap.2094-T1
Valid prediction for GlimmerHMM_glimmerT_54855-T1
Valid prediction for snap_scaffold_25-snap.2096-T1
Valid prediction for Augustus_model.g36407.t1
Valid prediction for snap_scaffold_25-snap.2117-T1
Valid prediction for Augustus_model.g36411.t1
Valid prediction for Augustus_model.g36410.t1

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

-building trellis in range 1 - 295055
-exon list size: 272


building trellis

0.4    
0.7    
1.1    
1.5    
1.8    
2.2    
2.6    
2.9    
3.3    
3.6    
4.0    
4.4    
4.7    
5.1    
5.5    
5.8    
6.2    
6.6    
6.9    
7.3    
7.7    
8.0    
8.4    
8.8    
9.1    
9.5    
9.9    
10.2    
10.6    
10.9    
11.3    
11.7    
12.0    
12.4    
12.8    
13.1    
13.5    
13.9    
14.2    
14.6    
15.0    
15.3    
15.7    
16.1    
16.4    
16.8    
17.2    
17.5    
17.9    
18.2    
18.6    
19.0    
19.3    
19.7    
20.1    
20.4    
20.8    
21.2    
21.5    
21.9    
22.3    
22.6    
23.0    
23.4    
23.7    
24.1    
24.5    
24.8    
25.2    
25.5    
25.9    
26.3    
26.6    
27.0    
27.4    
27.7    
28.1    
28.5    
28.8    
29.2    
29.6    
29.9    
30.3    
30.7    
31.0    
31.4    
31.8    
32.1    
32.5    
32.8    
33.2    
33.6    
33.9    
34.3    
34.7    
35.0    
35.4    
35.8    
36.1    
36.5    
36.9    
37.2    
37.6    
38.0    
38.3    
38.7    
39.1    
39.4    
39.8    
40.1    
40.5    
40.9    
41.2    
41.6    
42.0    
42.3    
42.7    
43.1    
43.4    
43.8    
44.2    
44.5    
44.9    
45.3    
45.6    
46.0    
46.4    
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    
53.6    
54.0    
54.4    
54.7    
55.1    
55.5    
55.8    
56.2    
56.6    
56.9    
57.3    
57.7    
58.0    
58.4    
58.8    
59.1    
59.5    
59.9    
60.2    
60.6    
60.9    
61.3    
61.7    
62.0    
62.4    
62.8    
63.1    
63.5    
63.9    
64.2    
64.6    
65.0    
65.3    
65.7    
66.1    
66.4    
66.8    
67.2    
67.5    
67.9    
68.2    
68.6    
69.0    
69.3    
69.7    
70.1    
70.4    
70.8    
71.2    
71.5    
71.9    
72.3    
72.6    
73.0    
73.4    
73.7    
74.1    
74.5    
74.8    
75.2    
75.5    
75.9    
76.3    
76.6    
77.0    
77.4    
77.7    
78.1    
78.5    
78.8    
79.2    
79.6    
79.9    
80.3    
80.7    
81.0    
81.4    
81.8    
82.1    
82.5    
82.8    
83.2    
83.6    
83.9    
84.3    
84.7    
85.0    
85.4    
85.8    
86.1    
86.5    
86.9    
87.2    
87.6    
88.0    
88.3    
88.7    
89.1    
89.4    
89.8    
90.1    
90.5    
90.9    
91.2    
91.6    
92.0    
92.3    
92.7    
93.1    
93.4    
93.8    
94.2    
94.5    
94.9    
95.3    
95.6    
96.0    
96.4    
96.7    
97.1    
97.4    
97.8    
98.2    
98.5    
98.9    
99.3    
99.6    
-found 35 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 33 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11861
-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
	-no exons in range 1 - 10632

-building DP trellis

-building trellis in range 252028 - 295055
-exon list size: 25


building trellis

3.7    
7.4    
11.1    
14.8    
18.5    
22.2    
25.9    
29.6    
33.3    
37.0    
40.7    
44.4    
48.1    
51.9    
55.6    
59.3    
63.0    
66.7    
70.4    
74.1    
77.8    
81.5    
85.2    
88.9    
92.6    
96.3    
-found 5 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 4 predictions persist after filtering for low support