-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_14182055-14400595

-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 GlimmerHMM_glimmerT_10808-T1
Couldn't classify 107322, 107397
Couldn't classify 110147, 110175
Sorry, prediction pasa_asmbl_43191.p1 fails validation.
(ACA)	 GG	107322-107397	GT	TGG
(GTG)	 AG	107668-107717	GT	AGG
(GGT)	 AG	107866-107997	GT	TGG
(GGT)	 AG	108086-108166	GT	AGG
(GTG)	 AG	108346-108477	GT	ATG
(CTA)	 AG	108581-108628	GT	GGG
(TTG)	 AG	108720-108776	GT	AGG
(GGT)	 AG	108932-108990	GT	AAG
(GTT)	 AG	109082-109161	GT	AGG
(GTG)	 AG	109321-109435	GT	AGG
(TGA)	 AG	109520-109585	GT	GAG
(GCA)	 AG	109770-109915	GT	GGG
(TCC)	 AG	110147-110175	GC	AGG
-recovered pasa_asmbl_43191.p1, internal, 107668, 107717
-recovered pasa_asmbl_43191.p1, internal, 107866, 107997
-recovered pasa_asmbl_43191.p1, internal, 108086, 108166
-recovered pasa_asmbl_43191.p1, internal, 108346, 108477
-recovered pasa_asmbl_43191.p1, internal, 108581, 108628
-recovered pasa_asmbl_43191.p1, internal, 108720, 108776
-recovered pasa_asmbl_43191.p1, internal, 108932, 108990
-recovered pasa_asmbl_43191.p1, internal, 109082, 109161
-recovered pasa_asmbl_43191.p1, internal, 109321, 109435
-recovered pasa_asmbl_43191.p1, internal, 109520, 109585
-recovered pasa_asmbl_43191.p1, internal, 109770, 109915
-recovered pasa_asmbl_43191.p1, internal, 110147, 110175
Valid prediction for snap_scaffold_4-snap.2884-T1
Couldn't classify 82070, 83380
Sorry, prediction pasa_asmbl_43189.p1 fails validation.
(GGT)	 AA	82070-83380	GG	GAG
Valid prediction for GlimmerHMM_glimmerT_10805-T1
Valid prediction for snap_scaffold_4-snap.2893-T1
Valid prediction for snap_scaffold_4-snap.2886-T1
Valid prediction for GeneMark_model.17541_t
Valid prediction for snap_scaffold_4-snap.2908-T1
Valid prediction for snap_scaffold_4-snap.2890-T1
Valid prediction for GlimmerHMM_glimmerT_10793-T1
Valid prediction for GlimmerHMM_glimmerT_10797-T1
Valid prediction for GeneMark_model.17535_t
Valid prediction for GeneMark_model.17537_t
Valid prediction for Augustus_model.g7131.t1
Valid prediction for snap_scaffold_4-snap.2897-T1
Valid prediction for GeneMark_model.17540_t
Valid prediction for snap_scaffold_4-snap.2910-T1
Valid prediction for GlimmerHMM_glimmerT_10809-T1
Valid prediction for snap_scaffold_4-snap.2887-T1
Couldn't classify 74194, 74351
Sorry, prediction pasa_asmbl_43188.p1 fails validation.
(ATG)	 CC	63866-63965	GT	AGG
(AGC)	 AG	64160-64248	GT	AGG
(GTT)	 AG	64396-64613	GT	AGG
(TAT)	 AG	64719-64850	GT	AGG
(ACC)	 AG	65084-65239	GT	AGG
(GTT)	 AG	65996-66169	GT	AAG
(GTG)	 AG	66321-66458	GT	ACG
(GAG)	 AG	68494-68574	GT	AAG
(GGC)	 AG	71559-71617	GT	TGG
(ACG)	 AG	71844-71894	GT	TGG
(GAA)	 AG	74194-74351	AA	GTA
-recovered pasa_asmbl_43188.p1, initial, 63866, 63965
-recovered pasa_asmbl_43188.p1, internal, 64160, 64248
-recovered pasa_asmbl_43188.p1, internal, 64396, 64613
-recovered pasa_asmbl_43188.p1, internal, 64719, 64850
-recovered pasa_asmbl_43188.p1, internal, 65084, 65239
-recovered pasa_asmbl_43188.p1, internal, 65996, 66169
-recovered pasa_asmbl_43188.p1, internal, 66321, 66458
-recovered pasa_asmbl_43188.p1, internal, 68494, 68574
-recovered pasa_asmbl_43188.p1, internal, 71559, 71617
-recovered pasa_asmbl_43188.p1, internal, 71844, 71894
Valid prediction for GlimmerHMM_glimmerT_10796-T1
Valid prediction for Augustus_model.g7120.t1
Valid prediction for snap_scaffold_4-snap.2906-T1
Valid prediction for Augustus_model.g7128.t1
Valid prediction for snap_scaffold_4-snap.2902-T1
Valid prediction for GeneMark_model.17547_t
Couldn't classify 110359, 110461
Couldn't classify 111387, 113049
Sorry, prediction pasa_asmbl_43193.p1 fails validation.
(GAG)	 CA	110359-110461	GT	AGG
(AGG)	 AG	110574-110728	GC	AGG
(AGG)	 AG	110892-111223	GT	AGG
(GGA)	 AG	111387-113049	TC	CGT
-recovered pasa_asmbl_43193.p1, internal, 110574, 110728
-recovered pasa_asmbl_43193.p1, internal, 110892, 111223
Valid prediction for snap_scaffold_4-snap.2883-T1
Valid prediction for snap_scaffold_4-snap.2889-T1
Valid prediction for snap_scaffold_4-snap.2891-T1
Valid prediction for GlimmerHMM_glimmerT_10800-T1
Valid prediction for HiQ_model.g7122.t1
Valid prediction for GeneMark_model.17558_t
Valid prediction for GlimmerHMM_glimmerT_10803-T1
Valid prediction for Augustus_model.g7119.t1
Valid prediction for GeneMark_model.17543_t
Valid prediction for snap_scaffold_4-snap.2888-T1
Valid prediction for GlimmerHMM_glimmerT_10792-T1
Valid prediction for GlimmerHMM_glimmerT_10799-T1
Valid prediction for Augustus_model.g7132.t1
Valid prediction for Augustus_model.g7133.t1
Valid prediction for Augustus_model.g7118.t1
Valid prediction for GeneMark_model.17554_t
Couldn't classify 113107, 113844
Sorry, prediction pasa_asmbl_43194.p1 fails validation.
(TCA)	 CC	113107-113844	GT	AGG
(GGA)	 AG	114038-114222	GT	CTG
(GGG)	 AG	114346-114450	GT	AGG
(CTC)	 AG	114763-114901	GT	AGG
(CTG)	 AG	115057-115170	GT	AGG
(CCT)	 AG	115507-116127	GA	GAG
-recovered pasa_asmbl_43194.p1, terminal, 115507, 116127
-recovered pasa_asmbl_43194.p1, internal, 114038, 114222
-recovered pasa_asmbl_43194.p1, internal, 114346, 114450
-recovered pasa_asmbl_43194.p1, internal, 114763, 114901
-recovered pasa_asmbl_43194.p1, internal, 115057, 115170
Valid prediction for GeneMark_model.17539_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: -)Valid prediction for GeneMark_model.17542_t
Valid prediction for snap_scaffold_4-snap.2909-T1
Valid prediction for GeneMark_model.17538_t
Valid prediction for GlimmerHMM_glimmerT_10804-T1
Valid prediction for Augustus_model.g7129.t1
Valid prediction for snap_scaffold_4-snap.2896-T1
Valid prediction for Augustus_model.g7123.t1
Valid prediction for GeneMark_model.17551_t
Valid prediction for snap_scaffold_4-snap.2894-T1
Valid prediction for GlimmerHMM_glimmerT_10794-T1
Valid prediction for snap_scaffold_4-snap.2882-T1
Valid prediction for Augustus_model.g7127.t1
Valid prediction for snap_scaffold_4-snap.2903-T1
Valid prediction for snap_scaffold_4-snap.2899-T1
Valid prediction for snap_scaffold_4-snap.2905-T1
Valid prediction for snap_scaffold_4-snap.2904-T1
Valid prediction for GlimmerHMM_glimmerT_10798-T1
Valid prediction for GeneMark_model.17544_t
Valid prediction for snap_scaffold_4-snap.2900-T1
Valid prediction for CodingQuarry_transcript_49118-T1
Couldn't classify 95234, 95311
Couldn't classify 96075, 96177
Sorry, prediction pasa_asmbl_42288.p1 fails validation.
(GAC)	 GC	95234-95311	GT	TGG
(GAT)	 AG	95546-95661	GT	GGG
(GTT)	 AG	96075-96177	TT	GCT
-recovered pasa_asmbl_42288.p1, internal, 95546, 95661
Couldn't classify 97950, 98102
Couldn't classify 98318, 98560
Sorry, prediction pasa_asmbl_41786.p1 fails validation.
(CTA)	 TC	97950-98102	GT	AGG
(GAG)	 AG	98318-98560	TG	ACT
Valid prediction for snap_scaffold_4-snap.2907-T1
Valid prediction for GeneMark_model.17556_t
Valid prediction for pasa_asmbl_41795.p1
Valid prediction for CodingQuarry_transcript_49117-T1
Valid prediction for snap_scaffold_4-snap.2895-T1
Valid prediction for pasa_asmbl_41789.p1
Valid prediction for GeneMark_model.17548_t
Valid prediction for snap_scaffold_4-snap.2901-T1
Valid prediction for GeneMark_model.17536_t
Valid prediction for Augustus_model.g7126.t1
Valid prediction for HiQ_model.g7130.t1
Valid prediction for GeneMark_model.17534_t
Couldn't classify 32951, 32971
Couldn't classify 38619, 38780
Sorry, prediction pasa_asmbl_42336.p1 fails validation.
(CTG)	 CG	32951-32971	GT	AGG
(ATC)	 AG	33204-33314	GT	AGG
(AGT)	 AG	33466-33525	GT	AGG
(GCT)	 AG	33671-33929	GT	GGG
(AGG)	 AG	34141-34302	GT	GGG
(AGA)	 AG	35572-35627	GT	AGG
(GCC)	 AG	36302-36449	GT	AGG
(ACA)	 AG	36658-36836	GT	AGG
(CAT)	 AG	37344-37478	GT	CAG
(CTG)	 AG	38619-38780	CC	GCC
-recovered pasa_asmbl_42336.p1, internal, 33204, 33314
-recovered pasa_asmbl_42336.p1, internal, 33466, 33525
-recovered pasa_asmbl_42336.p1, internal, 33671, 33929
-recovered pasa_asmbl_42336.p1, internal, 34141, 34302
-recovered pasa_asmbl_42336.p1, internal, 35572, 35627
-recovered pasa_asmbl_42336.p1, internal, 36302, 36449
-recovered pasa_asmbl_42336.p1, internal, 36658, 36836
-recovered pasa_asmbl_42336.p1, internal, 37344, 37478
Valid prediction for CodingQuarry_transcript_49116-T1
Valid prediction for GlimmerHMM_glimmerT_10807-T1
Valid prediction for pasa_asmbl_41783.p1
Valid prediction for HiQ_model.g7121.t1
Couldn't classify 29760, 29772
Couldn't classify 32159, 32212
Sorry, prediction pasa_asmbl_41794.p2 fails validation.
(CAA)	 CT	29760-29772	GT	CGG
(AGG)	 AG	29859-29928	GT	AGG
(CTA)	 AG	30125-30200	GT	AAG
(GTG)	 AG	30290-30415	GT	AGG
(TCT)	 AG	30799-30917	GT	GGG
(GAA)	 AG	31393-31520	GT	CGG
(TGA)	 AG	31741-31800	GT	GGG
(ATG)	 AG	31942-31979	GT	AGG
(GAC)	 AG	32159-32212	GA	AGG
add_exon() Sorry, pasa_asmbl_41794.p2 31942-31979-initial-1 is invalid.
-recovered pasa_asmbl_41794.p2, initial, 31942, 31979
-recovered pasa_asmbl_41794.p2, internal, 29859, 29928
-recovered pasa_asmbl_41794.p2, internal, 30125, 30200
-recovered pasa_asmbl_41794.p2, internal, 30290, 30415
-recovered pasa_asmbl_41794.p2, internal, 30799, 30917
-recovered pasa_asmbl_41794.p2, internal, 31393, 31520
-recovered pasa_asmbl_41794.p2, internal, 31741, 31800
-recovered pasa_asmbl_41794.p2, internal, 31942, 31979
Valid prediction for GeneMark_model.17545_t
Valid prediction for GeneMark_model.17555_t
Valid prediction for snap_scaffold_4-snap.2892-T1
Valid prediction for GlimmerHMM_glimmerT_10802-T1
Valid prediction for snap_scaffold_4-snap.2885-T1
Valid prediction for GeneMark_model.17557_t
Valid prediction for snap_scaffold_4-snap.2881-T1
Valid prediction for GlimmerHMM_glimmerT_10801-T1
Valid prediction for snap_scaffold_4-snap.2898-T1
Valid prediction for GeneMark_model.17552_t
Valid prediction for GeneMark_model.17546_t
Valid prediction for GeneMark_model.17549_t
Valid prediction for GlimmerHMM_glimmerT_10795-T1
Valid prediction for GeneMark_model.17553_t
Valid prediction for GlimmerHMM_glimmerT_10806-T1
Couldn't classify 96301, 96600
Couldn't classify 97235, 97338
Sorry, prediction pasa_asmbl_41787.p1 fails validation.
(CCC)	 AG	96301-96600	GT	AGG
(CTG)	 AG	96708-96793	GT	AGG
(GAT)	 AG	96981-97063	GT	AGG
(GGC)	 AG	97235-97338	AT	CCA
-recovered pasa_asmbl_41787.p1, internal, 96301, 96600
-recovered pasa_asmbl_41787.p1, internal, 96708, 96793
-recovered pasa_asmbl_41787.p1, internal, 96981, 97063
Valid prediction for Augustus_model.g7125.t1
Valid prediction for GlimmerHMM_glimmerT_10791-T1
Valid prediction for HiQ_model.g7124.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 174247, rend_intergenic: 174244  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206781, rend_intergenic: 201473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 218541
-exon list size: 407


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
1.5    
1.7    
2.0    
2.2    
2.4    
2.7    
2.9    
3.2    
3.4    
3.7    
3.9    
4.2    
4.4    
4.6    
4.9    
5.1    
5.4    
5.6    
5.9    
6.1    
6.4    
6.6    
6.8    
7.1    
7.3    
7.6    
7.8    
8.1    
8.3    
8.6    
8.8    
9.0    
9.3    
9.5    
9.8    
10.0    
10.3    
10.5    
10.8    
11.0    
11.2    
11.5    
11.7    
12.0    
12.2    
12.5    
12.7    
13.0    
13.2    
13.4    
13.7    
13.9    
14.2    
14.4    
14.7    
14.9    
15.2    
15.4    
15.6    
15.9    
16.1    
16.4    
16.6    
16.9    
17.1    
17.4    
17.6    
17.8    
18.1    
18.3    
18.6    
18.8    
19.1    
19.3    
19.6    
19.8    
20.0    
20.3    
20.5    
20.8    
21.0    
21.3    
21.5    
21.8    
22.0    
22.2    
22.5    
22.7    
23.0    
23.2    
23.5    
23.7    
24.0    
24.2    
24.4    
24.7    
24.9    
25.2    
25.4    
25.7    
25.9    
26.2    
26.4    
26.7    
26.9    
27.1    
27.4    
27.6    
27.9    
28.1    
28.4    
28.6    
28.9    
29.1    
29.3    
29.6    
29.8    
30.1    
30.3    
30.6    
30.8    
31.1    
31.3    
31.5    
31.8    
32.0    
32.3    
32.5    
32.8    
33.0    
33.3    
33.5    
33.7    
34.0    
34.2    
34.5    
34.7    
35.0    
35.2    
35.5    
35.7    
35.9    
36.2    
36.4    
36.7    
36.9    
37.2    
37.4    
37.7    
37.9    
38.1    
38.4    
38.6    
38.9    
39.1    
39.4    
39.6    
39.9    
40.1    
40.3    
40.6    
40.8    
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    
44.3    
44.5    
44.7    
45.0    
45.2    
45.5    
45.7    
46.0    
46.2    
46.5    
46.7    
46.9    
47.2    
47.4    
47.7    
47.9    
48.2    
48.4    
48.7    
48.9    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.1    
51.3    
51.6    
51.8    
52.1    
52.3    
52.6    
52.8    
53.1    
53.3    
53.5    
53.8    
54.0    
54.3    
54.5    
54.8    
55.0    
55.3    
55.5    
55.7    
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    
59.2    
59.4    
59.7    
59.9    
60.1    
60.4    
60.6    
60.9    
61.1    
61.4    
61.6    
61.9    
62.1    
62.3    
62.6    
62.8    
63.1    
63.3    
63.6    
63.8    
64.1    
64.3    
64.5    
64.8    
65.0    
65.3    
65.5    
65.8    
66.0    
66.3    
66.5    
66.7    
67.0    
67.2    
67.5    
67.7    
68.0    
68.2    
68.5    
68.7    
68.9    
69.2    
69.4    
69.7    
69.9    
70.2    
70.4    
70.7    
70.9    
71.1    
71.4    
71.6    
71.9    
72.1    
72.4    
72.6    
72.9    
73.1    
73.3    
73.6    
73.8    
74.1    
74.3    
74.6    
74.8    
75.1    
75.3    
75.6    
75.8    
76.0    
76.3    
76.5    
76.8    
77.0    
77.3    
77.5    
77.8    
78.0    
78.2    
78.5    
78.7    
79.0    
79.2    
79.5    
79.7    
80.0    
80.2    
80.4    
80.7    
80.9    
81.2    
81.4    
81.7    
81.9    
82.2    
82.4    
82.6    
82.9    
83.1    
83.4    
83.6    
83.9    
84.1    
84.4    
84.6    
84.8    
85.1    
85.3    
85.6    
85.8    
86.1    
86.3    
86.6    
86.8    
87.0    
87.3    
87.5    
87.8    
88.0    
88.3    
88.5    
88.8    
89.0    
89.2    
89.5    
89.7    
90.0    
90.2    
90.5    
90.7    
91.0    
91.2    
91.4    
91.7    
91.9    
92.2    
92.4    
92.7    
92.9    
93.2    
93.4    
93.6    
93.9    
94.1    
94.4    
94.6    
94.9    
95.1    
95.4    
95.6    
95.8    
96.1    
96.3    
96.6    
96.8    
97.1    
97.3    
97.6    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 19 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 174247, rend_intergenic: 174244  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206781, rend_intergenic: 201473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 57611
-exon list size: 39


building trellis

2.4    
4.9    
7.3    
9.8    
12.2    
14.6    
17.1    
19.5    
22.0    
24.4    
26.8    
29.3    
31.7    
34.1    
36.6    
39.0    
41.5    
43.9    
46.3    
48.8    
51.2    
53.7    
56.1    
58.5    
61.0    
63.4    
65.9    
68.3    
70.7    
73.2    
75.6    
78.0    
80.5    
82.9    
85.4    
87.8    
90.2    
92.7    
95.1    
97.6    
-found 2 predictions from path traversal

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

-building DP trellis

-building trellis in range 1 - 35779
-exon list size: 14


building trellis

6.2    
12.5    
18.8    
25.0    
31.2    
37.5    
43.8    
50.0    
56.2    
62.5    
68.8    
75.0    
81.2    
87.5    
93.8    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 9855 - 35779
-exon list size: 11


building trellis

7.7    
15.4    
23.1    
30.8    
38.5    
46.2    
53.8    
61.5    
69.2    
76.9    
84.6    
92.3    
-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 9855 - 35613
-exon list size: 10


building trellis

8.3    
16.7    
25.0    
33.3    
41.7    
50.0    
58.3    
66.7    
75.0    
83.3    
91.7    
-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 9855 - 31199
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-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 9855 - 25154
-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

-building DP trellis

-building trellis in range 9855 - 23522
-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

-building DP trellis

-building trellis in range 37657 - 57611
-exon list size: 17


building trellis

5.3    
10.5    
15.8    
21.1    
26.3    
31.6    
36.8    
42.1    
47.4    
52.6    
57.9    
63.2    
68.4    
73.7    
78.9    
84.2    
89.5    
94.7    
-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 37657 - 51027
-exon list size: 13


building trellis

6.7    
13.3    
20.0    
26.7    
33.3    
40.0    
46.7    
53.3    
60.0    
66.7    
73.3    
80.0    
86.7    
93.3    
-found 1 predictions from path traversal

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