-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_23/scaffold_23_4905389-5242703

-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.g34106.t1
Valid prediction for pasa_asmbl_31539.p1
Valid prediction for Augustus_model.g34101.t1
Valid prediction for GlimmerHMM_glimmerT_50995-T1
Valid prediction for GlimmerHMM_glimmerT_50992-T1
Valid prediction for Augustus_model.g34088.t1
Valid prediction for snap_scaffold_23-snap.909-T1
Valid prediction for snap_scaffold_23-snap.927-T1
Valid prediction for snap_scaffold_23-snap.922-T1
Valid prediction for GlimmerHMM_glimmerT_50976-T1
Sorry, intron length (4) is less than minimum required (10)
Couldn't classify 120112, 120367
Sorry, prediction pasa_asmbl_31546.p1 fails validation.
(GTC)	 AA	120112-120367	GT	AGG
(GAA)	 AG	122811-122878	GT	TGG
(ATG)	 AG	122976-123063	GT	AGG
(GTG)	 AG	124225-124311	GT	TGG
(GTA)	 AG	125152-125244	GT	ATG
(CAA)	 AG	126299-126355	GT	AGG
(GTC)	 AG	127935-128083	CC	GAC
-recovered pasa_asmbl_31546.p1, initial, 122976, 123063
-recovered pasa_asmbl_31546.p1, terminal, 127935, 128083
-recovered pasa_asmbl_31546.p1, internal, 122811, 122878
-recovered pasa_asmbl_31546.p1, internal, 122976, 123063
-recovered pasa_asmbl_31546.p1, internal, 124225, 124311
-recovered pasa_asmbl_31546.p1, internal, 125152, 125244
-recovered pasa_asmbl_31546.p1, internal, 126299, 126355
Valid prediction for GlimmerHMM_glimmerT_51002-T1
Valid prediction for snap_scaffold_23-snap.921-T1
Valid prediction for snap_scaffold_23-snap.912-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for snap_scaffold_23-snap.911-T1
Valid prediction for snap_scaffold_23-snap.905-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_23-snap.946-T1
Valid prediction for snap_scaffold_23-snap.915-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_50984-T1
Valid prediction for snap_scaffold_23-snap.917-T1
Valid prediction for GlimmerHMM_glimmerT_50986-T1
Valid prediction for snap_scaffold_23-snap.945-T1
Valid prediction for GlimmerHMM_glimmerT_50973-T1
Valid prediction for snap_scaffold_23-snap.910-T1
Valid prediction for CodingQuarry_transcript_35650-T1
Valid prediction for CodingQuarry_transcript_35648-T1
Valid prediction for Augustus_model.g34092.t1
Valid prediction for Augustus_model.g34099.t1
Valid prediction for GlimmerHMM_glimmerT_50980-T1
Valid prediction for Augustus_model.g34091.t1
Couldn't classify 292705, 293148
Sorry, prediction pasa_asmbl_31225.p1 fails validation.
(AAC)	 GT	292705-293148	GA	TTG
Valid prediction for Augustus_model.g34109.t1
Valid prediction for snap_scaffold_23-snap.947-T1
Valid prediction for snap_scaffold_23-snap.908-T1
Valid prediction for GlimmerHMM_glimmerT_50989-T1
Valid prediction for Augustus_model.g34095.t1
Valid prediction for snap_scaffold_23-snap.916-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_50975-T1
Valid prediction for HiQ_model.g34087.t1
Valid prediction for Augustus_model.g34094.t1
Valid prediction for GlimmerHMM_glimmerT_50974-T1
Valid prediction for snap_scaffold_23-snap.914-T1
Valid prediction for snap_scaffold_23-snap.929-T1
Valid prediction for Augustus_model.g34089.t1
Valid prediction for GlimmerHMM_glimmerT_50977-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for snap_scaffold_23-snap.941-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_23-snap.943-T1
Valid prediction for GlimmerHMM_glimmerT_50988-T1
Valid prediction for GlimmerHMM_glimmerT_50985-T1
Valid prediction for snap_scaffold_23-snap.931-T1
Valid prediction for snap_scaffold_23-snap.934-T1
Valid prediction for GlimmerHMM_glimmerT_51000-T1
Valid prediction for snap_scaffold_23-snap.919-T1
Valid prediction for Augustus_model.g34100.t1
Valid prediction for snap_scaffold_23-snap.938-T1
Valid prediction for Augustus_model.g34108.t1
Valid prediction for Augustus_model.g34097.t1
Valid prediction for GlimmerHMM_glimmerT_50997-T1
Valid prediction for GlimmerHMM_glimmerT_50993-T1
Valid prediction for GlimmerHMM_glimmerT_50999-T1
Valid prediction for snap_scaffold_23-snap.920-T1
Sorry, intron length (9) is less than minimum required (10)
Couldn't classify 37135, 37186
Sorry, prediction pasa_asmbl_30897.p1 fails validation.
(GCT)	 AA	37135-37186	GT	AGG
(AAA)	 AG	38889-39200	GT	AGG
(ACG)	 AG	39619-39678	GT	AGG
(GCA)	 AG	41501-41685	GA	AAG
-recovered pasa_asmbl_30897.p1, terminal, 41501, 41685
-recovered pasa_asmbl_30897.p1, internal, 38889, 39200
-recovered pasa_asmbl_30897.p1, internal, 39619, 39678
Couldn't classify 6861, 6951
Sorry, prediction pasa_asmbl_30903.p1 fails validation.
(GAC)	 GG	6861-6951	GT	AGG
(ATG)	 AG	7431-7514	GT	AGG
(ACC)	 AG	8660-8708	GT	CCG
(ACA)	 AG	10766-10833	GT	AGG
(TTA)	 AG	11450-11530	GT	CGG
(GCC)	 AG	11739-11863	AT	AGA
-recovered pasa_asmbl_30903.p1, initial, 7431, 7514
-recovered pasa_asmbl_30903.p1, terminal, 11739, 11863
-recovered pasa_asmbl_30903.p1, internal, 7431, 7514
-recovered pasa_asmbl_30903.p1, internal, 8660, 8708
-recovered pasa_asmbl_30903.p1, internal, 10766, 10833
-recovered pasa_asmbl_30903.p1, internal, 11450, 11530
Valid prediction for snap_scaffold_23-snap.935-T1
Valid prediction for HiQ_model.g34090.t1
Valid prediction for pasa_asmbl_30885.p1
Valid prediction for GlimmerHMM_glimmerT_50970-T1
Couldn't classify 172193, 172401
Sorry, prediction pasa_asmbl_30879.p1 fails validation.
(ACA)	 GG	172193-172401	GT	AAG
(GCA)	 AG	172655-172844	GT	AGG
(GCC)	 AG	173613-173753	GT	AGG
(GGT)	 AG	176374-176486	GT	AGG
(TGT)	 AG	176684-176756	TC	GAT
-recovered pasa_asmbl_30879.p1, terminal, 176684, 176756
-recovered pasa_asmbl_30879.p1, internal, 172655, 172844
-recovered pasa_asmbl_30879.p1, internal, 173613, 173753
-recovered pasa_asmbl_30879.p1, internal, 176374, 176486
Valid prediction for snap_scaffold_23-snap.918-T1
Valid prediction for GlimmerHMM_glimmerT_50996-T1
Valid prediction for GlimmerHMM_glimmerT_50978-T1
Valid prediction for snap_scaffold_23-snap.907-T1
Couldn't classify 67709, 67777
Sorry, prediction pasa_asmbl_30894.p1 fails validation.
(CGC)	 AC	67709-67777	GT	AGG
(GGT)	 AG	68007-68189	GT	AGG
(CTT)	 AG	69180-69321	GT	AGG
(ACA)	 AG	70016-70239	GT	AGG
(GAA)	 AG	70777-70904	GT	GTG
(ATA)	 AG	71007-71121	GT	ATG
(GAG)	 AG	71259-71366	GT	AGG
(GAC)	 AG	71439-71555	GT	AGG
(AAT)	 AG	72125-72598	GT	AGG
-recovered pasa_asmbl_30894.p1, terminal, 72125, 72598
-recovered pasa_asmbl_30894.p1, internal, 68007, 68189
-recovered pasa_asmbl_30894.p1, internal, 69180, 69321
-recovered pasa_asmbl_30894.p1, internal, 70016, 70239
-recovered pasa_asmbl_30894.p1, internal, 70777, 70904
-recovered pasa_asmbl_30894.p1, internal, 71007, 71121
-recovered pasa_asmbl_30894.p1, internal, 71259, 71366
-recovered pasa_asmbl_30894.p1, internal, 71439, 71555
-recovered pasa_asmbl_30894.p1, internal, 72125, 72598
Valid prediction for GlimmerHMM_glimmerT_50971-T1
Valid prediction for CodingQuarry_transcript_35652-T1
Valid prediction for snap_scaffold_23-snap.942-T1
Valid prediction for snap_scaffold_23-snap.926-T1
Valid prediction for GlimmerHMM_glimmerT_50983-T1
Valid prediction for HiQ_model.g34102.t1
Valid prediction for Augustus_model.g34084.t1
Valid prediction for GlimmerHMM_glimmerT_50987-T1
Valid prediction for CodingQuarry_transcript_35651-T1
Valid prediction for snap_scaffold_23-snap.940-T1
Valid prediction for snap_scaffold_23-snap.925-T1
Valid prediction for snap_scaffold_23-snap.924-T1
Valid prediction for GlimmerHMM_glimmerT_50990-T1
Valid prediction for GlimmerHMM_glimmerT_50969-T1
Valid prediction for Augustus_model.g34107.t1
Couldn't classify 158136, 158375
Couldn't classify 164098, 164258
Sorry, prediction pasa_asmbl_30880.p1 fails validation.
(CAG)	 GC	158136-158375	GT	AGG
(GGT)	 AG	159031-159191	GT	CTG
(TAT)	 AG	160378-160516	GT	AGG
(TTA)	 AG	160734-160812	GT	CGG
(TGG)	 AG	161125-161162	GT	CTG
(CAA)	 AG	162138-162209	GT	AGG
(AGG)	 AG	163751-163829	GT	TGG
(ATG)	 AG	164098-164258	TA	AGT
-recovered pasa_asmbl_30880.p1, internal, 159031, 159191
-recovered pasa_asmbl_30880.p1, internal, 160378, 160516
-recovered pasa_asmbl_30880.p1, internal, 160734, 160812
-recovered pasa_asmbl_30880.p1, internal, 161125, 161162
-recovered pasa_asmbl_30880.p1, internal, 162138, 162209
-recovered pasa_asmbl_30880.p1, internal, 163751, 163829
Valid prediction for GlimmerHMM_glimmerT_50982-T1
Valid prediction for snap_scaffold_23-snap.930-T1
Couldn't classify 14856, 14959
Couldn't classify 16465, 16514
Sorry, prediction pasa_asmbl_30902.p1 fails validation.
(GCA)	 AG	14856-14959	GT	GGG
(GGG)	 AG	16047-16243	GT	AGG
(GTC)	 AG	16465-16514	AT	AGA
-recovered pasa_asmbl_30902.p1, internal, 14856, 14959
-recovered pasa_asmbl_30902.p1, internal, 16047, 16243
Valid prediction for snap_scaffold_23-snap.923-T1
Valid prediction for GlimmerHMM_glimmerT_51001-T1
Valid prediction for snap_scaffold_23-snap.939-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_50994-T1
Valid prediction for snap_scaffold_23-snap.913-T1
Valid prediction for snap_scaffold_23-snap.928-T1
Valid prediction for snap_scaffold_23-snap.944-T1
Valid prediction for pasa_asmbl_30883.p1
Valid prediction for snap_scaffold_23-snap.936-T1
Valid prediction for Augustus_model.g34093.t1
Valid prediction for CodingQuarry_transcript_35653-T1
Valid prediction for Augustus_model.g34104.t1
Valid prediction for Augustus_model.g34105.t1
Valid prediction for HiQ_model.g34098.t1
Valid prediction for Augustus_model.g34086.t1
Valid prediction for snap_scaffold_23-snap.937-T1
Valid prediction for Augustus_model.g34103.t1
Valid prediction for snap_scaffold_23-snap.932-T1
Couldn't classify 21387, 21462
Couldn't classify 30640, 30735
Sorry, prediction pasa_asmbl_30901.p1 fails validation.
(GCC)	 CG	21387-21462	GT	AGG
(GGT)	 AG	23862-23991	GT	AAG
(CTC)	 AG	25571-25687	GT	ATG
(ATT)	 AG	25863-25935	GT	AGG
(GTG)	 AG	26277-26487	GT	AGG
(GTT)	 AG	26883-27086	GT	TGG
(GTG)	 AG	27545-27663	GT	AGG
(GAG)	 AG	30640-30735	AG	AAA
-recovered pasa_asmbl_30901.p1, internal, 23862, 23991
-recovered pasa_asmbl_30901.p1, internal, 25571, 25687
-recovered pasa_asmbl_30901.p1, internal, 25863, 25935
-recovered pasa_asmbl_30901.p1, internal, 26277, 26487
-recovered pasa_asmbl_30901.p1, internal, 26883, 27086
-recovered pasa_asmbl_30901.p1, internal, 27545, 27663
Couldn't classify 67143, 67227
Sorry, prediction pasa_asmbl_30895.p1 fails validation.
(ATG)	 CC	53154-53324	GT	CGG
(CCC)	 AG	54135-54330	GT	AGG
(GTT)	 AG	55078-55168	GT	AGG
(GAG)	 AG	57315-57400	GT	AGG
(AGT)	 AG	59617-59771	GT	AGG
(ATT)	 AG	60010-60111	GT	AGG
(GTG)	 AG	62637-62798	GT	AGG
(CAA)	 AG	64911-65032	GT	GGG
(GAA)	 AG	65155-65256	GT	ATG
(GAT)	 AG	65392-65478	GT	AGG
(GTT)	 AG	65597-65672	GT	AGG
(GAA)	 AG	65777-65886	GT	ATG
(GTA)	 AG	67143-67227	GG	AAG
-recovered pasa_asmbl_30895.p1, initial, 53154, 53324
-recovered pasa_asmbl_30895.p1, internal, 54135, 54330
-recovered pasa_asmbl_30895.p1, internal, 55078, 55168
-recovered pasa_asmbl_30895.p1, internal, 57315, 57400
-recovered pasa_asmbl_30895.p1, internal, 59617, 59771
-recovered pasa_asmbl_30895.p1, internal, 60010, 60111
-recovered pasa_asmbl_30895.p1, internal, 62637, 62798
-recovered pasa_asmbl_30895.p1, internal, 64911, 65032
-recovered pasa_asmbl_30895.p1, internal, 65155, 65256
-recovered pasa_asmbl_30895.p1, internal, 65392, 65478
-recovered pasa_asmbl_30895.p1, internal, 65597, 65672
-recovered pasa_asmbl_30895.p1, internal, 65777, 65886
Valid prediction for GlimmerHMM_glimmerT_50991-T1
Valid prediction for Augustus_model.g34085.t1
Valid prediction for GlimmerHMM_glimmerT_50998-T1
Valid prediction for Augustus_model.g34096.t1
Valid prediction for snap_scaffold_23-snap.906-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_23-snap.933-T1
Valid prediction for GlimmerHMM_glimmerT_50972-T1
Valid prediction for GlimmerHMM_glimmerT_50979-T1
Valid prediction for GlimmerHMM_glimmerT_50981-T1

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

-building trellis in range 1 - 337315
-exon list size: 406


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
1.5    
1.7    
2.0    
2.2    
2.5    
2.7    
2.9    
3.2    
3.4    
3.7    
3.9    
4.2    
4.4    
4.7    
4.9    
5.1    
5.4    
5.6    
5.9    
6.1    
6.4    
6.6    
6.9    
7.1    
7.4    
7.6    
7.8    
8.1    
8.3    
8.6    
8.8    
9.1    
9.3    
9.6    
9.8    
10.0    
10.3    
10.5    
10.8    
11.0    
11.3    
11.5    
11.8    
12.0    
12.3    
12.5    
12.7    
13.0    
13.2    
13.5    
13.7    
14.0    
14.2    
14.5    
14.7    
15.0    
15.2    
15.4    
15.7    
15.9    
16.2    
16.4    
16.7    
16.9    
17.2    
17.4    
17.6    
17.9    
18.1    
18.4    
18.6    
18.9    
19.1    
19.4    
19.6    
19.9    
20.1    
20.3    
20.6    
20.8    
21.1    
21.3    
21.6    
21.8    
22.1    
22.3    
22.5    
22.8    
23.0    
23.3    
23.5    
23.8    
24.0    
24.3    
24.5    
24.8    
25.0    
25.2    
25.5    
25.7    
26.0    
26.2    
26.5    
26.7    
27.0    
27.2    
27.5    
27.7    
27.9    
28.2    
28.4    
28.7    
28.9    
29.2    
29.4    
29.7    
29.9    
30.1    
30.4    
30.6    
30.9    
31.1    
31.4    
31.6    
31.9    
32.1    
32.4    
32.6    
32.8    
33.1    
33.3    
33.6    
33.8    
34.1    
34.3    
34.6    
34.8    
35.0    
35.3    
35.5    
35.8    
36.0    
36.3    
36.5    
36.8    
37.0    
37.3    
37.5    
37.7    
38.0    
38.2    
38.5    
38.7    
39.0    
39.2    
39.5    
39.7    
40.0    
40.2    
40.4    
40.7    
40.9    
41.2    
41.4    
41.7    
41.9    
42.2    
42.4    
42.6    
42.9    
43.1    
43.4    
43.6    
43.9    
44.1    
44.4    
44.6    
44.9    
45.1    
45.3    
45.6    
45.8    
46.1    
46.3    
46.6    
46.8    
47.1    
47.3    
47.5    
47.8    
48.0    
48.3    
48.5    
48.8    
49.0    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
51.0    
51.2    
51.5    
51.7    
52.0    
52.2    
52.5    
52.7    
52.9    
53.2    
53.4    
53.7    
53.9    
54.2    
54.4    
54.7    
54.9    
55.1    
55.4    
55.6    
55.9    
56.1    
56.4    
56.6    
56.9    
57.1    
57.4    
57.6    
57.8    
58.1    
58.3    
58.6    
58.8    
59.1    
59.3    
59.6    
59.8    
60.0    
60.3    
60.5    
60.8    
61.0    
61.3    
61.5    
61.8    
62.0    
62.3    
62.5    
62.7    
63.0    
63.2    
63.5    
63.7    
64.0    
64.2    
64.5    
64.7    
65.0    
65.2    
65.4    
65.7    
65.9    
66.2    
66.4    
66.7    
66.9    
67.2    
67.4    
67.6    
67.9    
68.1    
68.4    
68.6    
68.9    
69.1    
69.4    
69.6    
69.9    
70.1    
70.3    
70.6    
70.8    
71.1    
71.3    
71.6    
71.8    
72.1    
72.3    
72.5    
72.8    
73.0    
73.3    
73.5    
73.8    
74.0    
74.3    
74.5    
74.8    
75.0    
75.2    
75.5    
75.7    
76.0    
76.2    
76.5    
76.7    
77.0    
77.2    
77.5    
77.7    
77.9    
78.2    
78.4    
78.7    
78.9    
79.2    
79.4    
79.7    
79.9    
80.1    
80.4    
80.6    
80.9    
81.1    
81.4    
81.6    
81.9    
82.1    
82.4    
82.6    
82.8    
83.1    
83.3    
83.6    
83.8    
84.1    
84.3    
84.6    
84.8    
85.0    
85.3    
85.5    
85.8    
86.0    
86.3    
86.5    
86.8    
87.0    
87.3    
87.5    
87.7    
88.0    
88.2    
88.5    
88.7    
89.0    
89.2    
89.5    
89.7    
90.0    
90.2    
90.4    
90.7    
90.9    
91.2    
91.4    
91.7    
91.9    
92.2    
92.4    
92.6    
92.9    
93.1    
93.4    
93.6    
93.9    
94.1    
94.4    
94.6    
94.9    
95.1    
95.3    
95.6    
95.8    
96.1    
96.3    
96.6    
96.8    
97.1    
97.3    
97.5    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 37 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 1 - 11991
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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
	-no exons in range 1 - 10154