-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_11/scaffold_11_14167099-14503120

-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.49823_t
Valid prediction for GeneMark_model.49812_t
Valid prediction for snap_scaffold_11-snap.2994-T1
Valid prediction for GeneMark_model.49821_t
Valid prediction for GlimmerHMM_glimmerT_28862-T1
Valid prediction for snap_scaffold_11-snap.2996-T1
Valid prediction for GeneMark_model.49816_t
Valid prediction for GlimmerHMM_glimmerT_28850-T1
Valid prediction for GeneMark_model.49813_t
Valid prediction for GeneMark_model.49824_t
Valid prediction for Augustus_model.g19256.t1
Valid prediction for GeneMark_model.49808_t
Valid prediction for GlimmerHMM_glimmerT_28846-T1
Valid prediction for GlimmerHMM_glimmerT_28857-T1
Valid prediction for snap_scaffold_11-snap.2992-T1
Valid prediction for GeneMark_model.49828_t
Valid prediction for GeneMark_model.49815_t
Valid prediction for GlimmerHMM_glimmerT_28849-T1
Valid prediction for snap_scaffold_11-snap.2995-T1
Valid prediction for GeneMark_model.49809_t
Valid prediction for GeneMark_model.49820_t

-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: -)Couldn't classify 72407, 72441
Sorry, prediction pasa_asmbl_7142.p1 fails validation.
(TTA)	 AG	72407-72441	GT	AGG
(GGG)	 AG	72678-72765	GT	GTG
(GAC)	 AG	72849-72904	GT	AGG
(CCG)	 AG	73633-73792	AC	GAA
-recovered pasa_asmbl_7142.p1, terminal, 73633, 73792
-recovered pasa_asmbl_7142.p1, internal, 72407, 72441
-recovered pasa_asmbl_7142.p1, internal, 72678, 72765
-recovered pasa_asmbl_7142.p1, internal, 72849, 72904
Valid prediction for Augustus_model.g19257.t1
Valid prediction for GeneMark_model.49827_t
Valid prediction for snap_scaffold_11-snap.2997-T1
Valid prediction for GlimmerHMM_glimmerT_28854-T1
Valid prediction for GlimmerHMM_glimmerT_28851-T1
Valid prediction for GeneMark_model.49818_t
Couldn't classify 89315, 89503
Sorry, prediction pasa_asmbl_7140.p1 fails validation.
(CAG)	 GG	89315-89503	GT	AGG
(CTT)	 AG	90324-90486	GT	AGG
(AGA)	 AG	90694-90769	GT	AGG
(TCC)	 AG	91039-91204	GC	GAG
add_exon() Sorry, pasa_asmbl_7140.p1 90324-90486-terminal-3 is invalid.
-recovered pasa_asmbl_7140.p1, terminal, 90324, 90486
-recovered pasa_asmbl_7140.p1, terminal, 91039, 91204
-recovered pasa_asmbl_7140.p1, internal, 90324, 90486
-recovered pasa_asmbl_7140.p1, internal, 90694, 90769
-recovered pasa_asmbl_7140.p1, internal, 91039, 91204
Valid prediction for GeneMark_model.49825_t
Valid prediction for snap_scaffold_11-snap.3005-T1
Valid prediction for GeneMark_model.49811_t
Valid prediction for Augustus_model.g19254.t1
Valid prediction for snap_scaffold_11-snap.3004-T1
Couldn't classify 325010, 325128
Sorry, prediction pasa_asmbl_7136.p1 fails validation.
(ACT)	 AC	325010-325128	GT	GGG
(GGC)	 AG	325394-325549	GT	GCG
(CAC)	 AG	325827-325951	GT	TGG
(CCC)	 AG	326105-326232	GT	TGG
(ACT)	 AG	326430-326519	GT	TCG
(AAC)	 AG	326612-326701	GT	AGG
(ATC)	 AG	326897-327041	GT	CGG
(CAA)	 AG	327289-327469	GT	TGG
(GGA)	 AG	327603-327766	GT	CGG
(CTG)	 AG	327881-327957	GT	AGG
(GGT)	 AG	328228-328371	CA	AAC
-recovered pasa_asmbl_7136.p1, terminal, 328228, 328371
-recovered pasa_asmbl_7136.p1, internal, 325394, 325549
-recovered pasa_asmbl_7136.p1, internal, 325827, 325951
-recovered pasa_asmbl_7136.p1, internal, 326105, 326232
-recovered pasa_asmbl_7136.p1, internal, 326430, 326519
-recovered pasa_asmbl_7136.p1, internal, 326612, 326701
-recovered pasa_asmbl_7136.p1, internal, 326897, 327041
-recovered pasa_asmbl_7136.p1, internal, 327289, 327469
-recovered pasa_asmbl_7136.p1, internal, 327603, 327766
-recovered pasa_asmbl_7136.p1, internal, 327881, 327957
Valid prediction for GlimmerHMM_glimmerT_28858-T1
Valid prediction for HiQ_model.g19265.t1
Valid prediction for GeneMark_model.49817_t
Valid prediction for HiQ_model.g19255.t1
Valid prediction for GlimmerHMM_glimmerT_28847-T1
Valid prediction for snap_scaffold_11-snap.2998-T1
Couldn't classify 31576, 31719
Sorry, prediction pasa_asmbl_7145.p1 fails validation.
(ATG)	 TC	30384-30527	GT	AGG
(AAA)	 AG	30864-31036	GT	AGG
(TCG)	 AG	31168-31306	GT	AGG
(GTG)	 AG	31576-31719	TA	CCT
-recovered pasa_asmbl_7145.p1, initial, 30384, 30527
-recovered pasa_asmbl_7145.p1, internal, 30864, 31036
-recovered pasa_asmbl_7145.p1, internal, 31168, 31306
Valid prediction for snap_scaffold_11-snap.3003-T1
Valid prediction for Augustus_model.g19262.t1
Valid prediction for GeneMark_model.49814_t
Valid prediction for GlimmerHMM_glimmerT_28860-T1
Valid prediction for GlimmerHMM_glimmerT_28853-T1
Valid prediction for pasa_asmbl_7143.p2
Valid prediction for GeneMark_model.49819_t
Couldn't classify 86884, 87030
Couldn't classify 87951, 88148
Sorry, prediction pasa_asmbl_7141.p1 fails validation.
(AAC)	 GC	86884-87030	GT	AGG
(GCC)	 AG	87951-88148	GC	GGG
-recovered pasa_asmbl_7141.p1, internal, 87951, 88148
Valid prediction for pasa_asmbl_7146.p1
Valid prediction for GlimmerHMM_glimmerT_28844-T1
Valid prediction for CodingQuarry_transcript_8270-T1
Valid prediction for GlimmerHMM_glimmerT_28864-T1
Valid prediction for GeneMark_model.49833_t
Valid prediction for CodingQuarry_transcript_8271-T1
Valid prediction for Augustus_model.g19263.t1
Valid prediction for HiQ_model.g19259.t1
Valid prediction for GeneMark_model.49807_t
Valid prediction for GlimmerHMM_glimmerT_28863-T1
Valid prediction for Augustus_model.g19260.t1
Valid prediction for GlimmerHMM_glimmerT_28861-T1
Valid prediction for snap_scaffold_11-snap.3002-T1
Valid prediction for snap_scaffold_11-snap.2990-T1
Valid prediction for snap_scaffold_11-snap.3000-T1
Valid prediction for Augustus_model.g19261.t1
Valid prediction for GlimmerHMM_glimmerT_28848-T1
Valid prediction for GeneMark_model.49829_t
Valid prediction for GlimmerHMM_glimmerT_28852-T1
Valid prediction for CodingQuarry_transcript_8269-T1
Valid prediction for GlimmerHMM_glimmerT_28856-T1
Valid prediction for Augustus_model.g19264.t1
Valid prediction for GlimmerHMM_glimmerT_28843-T1
Valid prediction for snap_scaffold_11-snap.2993-T1
Valid prediction for GlimmerHMM_glimmerT_28859-T1
Valid prediction for CodingQuarry_transcript_8272-T1
Valid prediction for snap_scaffold_11-snap.2991-T1
Valid prediction for GeneMark_model.49831_t
Valid prediction for snap_scaffold_11-snap.3006-T1
Valid prediction for GeneMark_model.49826_t
Valid prediction for GeneMark_model.49830_t
Valid prediction for GlimmerHMM_glimmerT_28855-T1
Valid prediction for GeneMark_model.49822_t
Valid prediction for Augustus_model.g19258.t1
Valid prediction for snap_scaffold_11-snap.2999-T1
Valid prediction for snap_scaffold_11-snap.3001-T1
Valid prediction for GlimmerHMM_glimmerT_28845-T1

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

-building trellis in range 1 - 336022
-exon list size: 344


building trellis

0.3    
0.6    
0.9    
1.2    
1.4    
1.7    
2.0    
2.3    
2.6    
2.9    
3.2    
3.5    
3.8    
4.0    
4.3    
4.6    
4.9    
5.2    
5.5    
5.8    
6.1    
6.4    
6.6    
6.9    
7.2    
7.5    
7.8    
8.1    
8.4    
8.7    
9.0    
9.2    
9.5    
9.8    
10.1    
10.4    
10.7    
11.0    
11.3    
11.6    
11.8    
12.1    
12.4    
12.7    
13.0    
13.3    
13.6    
13.9    
14.2    
14.5    
14.7    
15.0    
15.3    
15.6    
15.9    
16.2    
16.5    
16.8    
17.1    
17.3    
17.6    
17.9    
18.2    
18.5    
18.8    
19.1    
19.4    
19.7    
19.9    
20.2    
20.5    
20.8    
21.1    
21.4    
21.7    
22.0    
22.3    
22.5    
22.8    
23.1    
23.4    
23.7    
24.0    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
26.9    
27.2    
27.5    
27.7    
28.0    
28.3    
28.6    
28.9    
29.2    
29.5    
29.8    
30.1    
30.3    
30.6    
30.9    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
32.9    
33.2    
33.5    
33.8    
34.1    
34.4    
34.7    
35.0    
35.3    
35.5    
35.8    
36.1    
36.4    
36.7    
37.0    
37.3    
37.6    
37.9    
38.2    
38.4    
38.7    
39.0    
39.3    
39.6    
39.9    
40.2    
40.5    
40.8    
41.0    
41.3    
41.6    
41.9    
42.2    
42.5    
42.8    
43.1    
43.4    
43.6    
43.9    
44.2    
44.5    
44.8    
45.1    
45.4    
45.7    
46.0    
46.2    
46.5    
46.8    
47.1    
47.4    
47.7    
48.0    
48.3    
48.6    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.4    
51.7    
52.0    
52.3    
52.6    
52.9    
53.2    
53.5    
53.8    
54.0    
54.3    
54.6    
54.9    
55.2    
55.5    
55.8    
56.1    
56.4    
56.6    
56.9    
57.2    
57.5    
57.8    
58.1    
58.4    
58.7    
59.0    
59.2    
59.5    
59.8    
60.1    
60.4    
60.7    
61.0    
61.3    
61.6    
61.8    
62.1    
62.4    
62.7    
63.0    
63.3    
63.6    
63.9    
64.2    
64.5    
64.7    
65.0    
65.3    
65.6    
65.9    
66.2    
66.5    
66.8    
67.1    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.1    
69.4    
69.7    
69.9    
70.2    
70.5    
70.8    
71.1    
71.4    
71.7    
72.0    
72.3    
72.5    
72.8    
73.1    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
76.0    
76.3    
76.6    
76.9    
77.2    
77.5    
77.7    
78.0    
78.3    
78.6    
78.9    
79.2    
79.5    
79.8    
80.1    
80.3    
80.6    
80.9    
81.2    
81.5    
81.8    
82.1    
82.4    
82.7    
82.9    
83.2    
83.5    
83.8    
84.1    
84.4    
84.7    
85.0    
85.3    
85.5    
85.8    
86.1    
86.4    
86.7    
87.0    
87.3    
87.6    
87.9    
88.2    
88.4    
88.7    
89.0    
89.3    
89.6    
89.9    
90.2    
90.5    
90.8    
91.0    
91.3    
91.6    
91.9    
92.2    
92.5    
92.8    
93.1    
93.4    
93.6    
93.9    
94.2    
94.5    
94.8    
95.1    
95.4    
95.7    
96.0    
96.2    
96.5    
96.8    
97.1    
97.4    
97.7    
98.0    
98.3    
98.6    
98.8    
99.1    
99.4    
99.7    
-found 15 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support