-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_15/scaffold_15_14115260-14342030

-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_37360-T1
Valid prediction for HiQ_model.g24893.t1
Valid prediction for snap_scaffold_15-snap.2861-T1
Valid prediction for CodingQuarry_transcript_18223-T1
Valid prediction for snap_scaffold_15-snap.2842-T1
Valid prediction for CodingQuarry_transcript_18221-T1
Valid prediction for GlimmerHMM_glimmerT_37336-T1
Valid prediction for GlimmerHMM_glimmerT_37349-T1
Valid prediction for Augustus_model.g24883.t1
Valid prediction for snap_scaffold_15-snap.2848-T1
Valid prediction for snap_scaffold_15-snap.2857-T1
Valid prediction for GlimmerHMM_glimmerT_37341-T1
Valid prediction for snap_scaffold_15-snap.2863-T1
Valid prediction for snap_scaffold_15-snap.2828-T1
Valid prediction for snap_scaffold_15-snap.2840-T1
Valid prediction for GlimmerHMM_glimmerT_37358-T1
Valid prediction for snap_scaffold_15-snap.2834-T1
Valid prediction for HiQ_model.g24898.t1
Valid prediction for CodingQuarry_transcript_18222-T1
Valid prediction for snap_scaffold_15-snap.2833-T1
Valid prediction for snap_scaffold_15-snap.2850-T1
Valid prediction for GlimmerHMM_glimmerT_37357-T1
Valid prediction for snap_scaffold_15-snap.2827-T1
Valid prediction for snap_scaffold_15-snap.2824-T1
Valid prediction for GlimmerHMM_glimmerT_37340-T1
Valid prediction for GlimmerHMM_glimmerT_37346-T1
Valid prediction for Augustus_model.g24890.t1
Valid prediction for GlimmerHMM_glimmerT_37339-T1
Valid prediction for Augustus_model.g24887.t1
Couldn't classify 194270, 194358
Sorry, prediction pasa_asmbl_15675.p1 fails validation.
(ATC)	 CC	194270-194358	GT	AGG
(TAA)	 AG	194967-195031	GT	AAG
(ATG)	 AG	196225-196409	TA	GAT
-recovered pasa_asmbl_15675.p1, terminal, 196225, 196409
-recovered pasa_asmbl_15675.p1, internal, 194967, 195031
Valid prediction for snap_scaffold_15-snap.2835-T1
Valid prediction for GlimmerHMM_glimmerT_37342-T1
Valid prediction for GlimmerHMM_glimmerT_37335-T1
Valid prediction for GlimmerHMM_glimmerT_37337-T1
Valid prediction for Augustus_model.g24889.t1
Valid prediction for snap_scaffold_15-snap.2847-T1
Valid prediction for snap_scaffold_15-snap.2852-T1
Valid prediction for snap_scaffold_15-snap.2867-T1
Valid prediction for snap_scaffold_15-snap.2821-T1
Valid prediction for snap_scaffold_15-snap.2830-T1
Valid prediction for snap_scaffold_15-snap.2862-T1
Valid prediction for snap_scaffold_15-snap.2841-T1
Valid prediction for snap_scaffold_15-snap.2846-T1
Valid prediction for pasa_asmbl_15674.p1
Valid prediction for Augustus_model.g24891.t1
Valid prediction for snap_scaffold_15-snap.2843-T1
Valid prediction for GlimmerHMM_glimmerT_37353-T1
Valid prediction for Augustus_model.g24888.t1
Valid prediction for Augustus_model.g24899.t1
Couldn't classify 107468, 107746
Couldn't classify 110969, 111075
Sorry, prediction pasa_asmbl_15670.p1 fails validation.
(CAA)	 TG	107468-107746	GT	AGG
(GTT)	 AG	107916-108084	GT	AGG
(GGC)	 AG	110349-110429	GT	AGG
(GCT)	 AG	110969-111075	GG	AAG
-recovered pasa_asmbl_15670.p1, internal, 107916, 108084
-recovered pasa_asmbl_15670.p1, internal, 110349, 110429
Valid prediction for Augustus_model.g24880.t1
Valid prediction for pasa_asmbl_15673.p1
Valid prediction for GlimmerHMM_glimmerT_37345-T1
Valid prediction for GlimmerHMM_glimmerT_37338-T1
Couldn't classify 201582, 202540
Sorry, prediction pasa_asmbl_15677.p1 fails validation.
(GCC)	 AG	201582-202540	GT	AGG
(GTT)	 AG	202834-203000	GT	AGG
(GGA)	 AG	204156-204310	GT	AGG
(GCC)	 AG	205068-205232	CA	GAC
-recovered pasa_asmbl_15677.p1, terminal, 205068, 205232
-recovered pasa_asmbl_15677.p1, internal, 201582, 202540
-recovered pasa_asmbl_15677.p1, internal, 202834, 203000
-recovered pasa_asmbl_15677.p1, internal, 204156, 204310
Valid prediction for HiQ_model.g24896.t1
Valid prediction for snap_scaffold_15-snap.2832-T1
Valid prediction for GlimmerHMM_glimmerT_37334-T1
Valid prediction for GlimmerHMM_glimmerT_37356-T1
Valid prediction for GlimmerHMM_glimmerT_37347-T1
Valid prediction for GlimmerHMM_glimmerT_37343-T1
Valid prediction for CodingQuarry_transcript_18224-T1
Valid prediction for snap_scaffold_15-snap.2837-T1
Couldn't classify 119915, 120104
Sorry, prediction pasa_asmbl_15671.p1 fails validation.
(GTG)	 TA	119915-120104	GT	AGG
(GAA)	 AG	122942-123075	CA	AGC
-recovered pasa_asmbl_15671.p1, terminal, 122942, 123075

-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 43711, 43731
Sorry, prediction pasa_asmbl_14706.p1 fails validation.
(CCC)	 CC	43711-43731	GT	AGG
(ACG)	 AG	43944-44102	GT	AGG
(TCG)	 AG	44282-44365	GT	CGG
(GCT)	 AG	44451-44599	GT	AGG
(GTC)	 AG	44832-44937	GT	AGG
(GAC)	 AG	45063-45131	CC	AAC
-recovered pasa_asmbl_14706.p1, terminal, 45063, 45131
-recovered pasa_asmbl_14706.p1, internal, 43944, 44102
-recovered pasa_asmbl_14706.p1, internal, 44282, 44365
-recovered pasa_asmbl_14706.p1, internal, 44451, 44599
-recovered pasa_asmbl_14706.p1, internal, 44832, 44937
Valid prediction for Augustus_model.g24882.t1
Valid prediction for snap_scaffold_15-snap.2822-T1
Valid prediction for GlimmerHMM_glimmerT_37348-T1
Valid prediction for snap_scaffold_15-snap.2831-T1
Valid prediction for snap_scaffold_15-snap.2829-T1
Valid prediction for snap_scaffold_15-snap.2839-T1
Valid prediction for snap_scaffold_15-snap.2838-T1
Valid prediction for GlimmerHMM_glimmerT_37354-T1
Valid prediction for Augustus_model.g24895.t1
Couldn't classify 19130, 19225
Sorry, prediction pasa_asmbl_14719.p1 fails validation.
(ATG)	 CG	11893-12084	GT	AGG
(ACT)	 AG	13291-13411	GT	GGG
(GGA)	 AG	14213-14304	GT	TGG
(GTT)	 AG	15478-15648	GT	AGG
(GAG)	 AG	16092-16286	GT	AGG
(AGC)	 AG	17028-17147	GT	ACG
(TTA)	 AG	17721-17795	GT	AGG
(CTG)	 AG	18813-18905	GT	AGG
(ATG)	 AG	19130-19225	GT	AGG
-recovered pasa_asmbl_14719.p1, initial, 11893, 12084
-recovered pasa_asmbl_14719.p1, initial, 19130, 19225
-recovered pasa_asmbl_14719.p1, internal, 13291, 13411
-recovered pasa_asmbl_14719.p1, internal, 14213, 14304
-recovered pasa_asmbl_14719.p1, internal, 15478, 15648
-recovered pasa_asmbl_14719.p1, internal, 16092, 16286
-recovered pasa_asmbl_14719.p1, internal, 17028, 17147
-recovered pasa_asmbl_14719.p1, internal, 17721, 17795
-recovered pasa_asmbl_14719.p1, internal, 18813, 18905
-recovered pasa_asmbl_14719.p1, internal, 19130, 19225
Valid prediction for snap_scaffold_15-snap.2854-T1
Valid prediction for snap_scaffold_15-snap.2825-T1
Valid prediction for snap_scaffold_15-snap.2856-T1
Valid prediction for snap_scaffold_15-snap.2853-T1
Valid prediction for Augustus_model.g24897.t1
Valid prediction for Augustus_model.g24894.t1
Valid prediction for GlimmerHMM_glimmerT_37359-T1
Valid prediction for GlimmerHMM_glimmerT_37355-T1
Couldn't classify 63806, 63842
Sorry, prediction pasa_asmbl_14703.p1 fails validation.
(GAT)	 CA	63806-63842	GT	AGG
(AGG)	 AG	64113-64157	GT	AGG
(GCA)	 AG	64850-64969	GT	GGG
(TTT)	 AG	66920-67000	GT	AGG
(ACC)	 AG	67772-67890	GT	AGG
(GTA)	 AG	68092-68336	GT	AGG
(CGC)	 AG	68437-68745	GT	AGG
(ATA)	 AG	69030-69400	GT	AGG
(GCA)	 AG	69604-70052	AG	GAA
-recovered pasa_asmbl_14703.p1, terminal, 69604, 70052
-recovered pasa_asmbl_14703.p1, internal, 64113, 64157
-recovered pasa_asmbl_14703.p1, internal, 64850, 64969
-recovered pasa_asmbl_14703.p1, internal, 66920, 67000
-recovered pasa_asmbl_14703.p1, internal, 67772, 67890
-recovered pasa_asmbl_14703.p1, internal, 68092, 68336
-recovered pasa_asmbl_14703.p1, internal, 68437, 68745
-recovered pasa_asmbl_14703.p1, internal, 69030, 69400
Valid prediction for snap_scaffold_15-snap.2868-T1
Valid prediction for CodingQuarry_transcript_18225-T1
Valid prediction for snap_scaffold_15-snap.2845-T1
Valid prediction for Augustus_model.g24901.t1
Valid prediction for snap_scaffold_15-snap.2836-T1
Valid prediction for GlimmerHMM_glimmerT_37344-T1
Valid prediction for Augustus_model.g24886.t1
Valid prediction for snap_scaffold_15-snap.2865-T1
Valid prediction for Augustus_model.g24881.t1
Valid prediction for snap_scaffold_15-snap.2826-T1
Valid prediction for Augustus_model.g24885.t1
Valid prediction for Augustus_model.g24884.t1
Valid prediction for GlimmerHMM_glimmerT_37351-T1
Valid prediction for Augustus_model.g24892.t1
Valid prediction for snap_scaffold_15-snap.2864-T1
Valid prediction for GlimmerHMM_glimmerT_37350-T1
Valid prediction for snap_scaffold_15-snap.2860-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_15-snap.2855-T1
Couldn't classify 36888, 37018
Sorry, prediction pasa_asmbl_14709.p2 fails validation.
(ATG)	 TC	34311-34463	GT	AGG
(ATC)	 AG	35549-35672	GT	CGG
(TGA)	 AG	36888-37018	CA	GGC
-recovered pasa_asmbl_14709.p2, initial, 34311, 34463
-recovered pasa_asmbl_14709.p2, internal, 35549, 35672
Valid prediction for snap_scaffold_15-snap.2858-T1
Valid prediction for GlimmerHMM_glimmerT_37352-T1
Couldn't classify 38370, 38429
Couldn't classify 43105, 43193
Sorry, prediction pasa_asmbl_14707.p1 fails validation.
(CCA)	 GA	38370-38429	GT	GGG
(GAG)	 AG	39744-39906	GT	TGG
(GTT)	 AG	40038-40101	GT	TGG
(GGA)	 AG	40369-40523	GT	AGG
(AGG)	 AG	40922-41043	GT	AGG
(CAG)	 AG	41957-42037	GT	CTG
(GAC)	 AG	42492-42579	GT	TGG
(ACC)	 AG	43105-43193	GC	CGG
-recovered pasa_asmbl_14707.p1, internal, 39744, 39906
-recovered pasa_asmbl_14707.p1, internal, 40038, 40101
-recovered pasa_asmbl_14707.p1, internal, 40369, 40523
-recovered pasa_asmbl_14707.p1, internal, 40922, 41043
-recovered pasa_asmbl_14707.p1, internal, 41957, 42037
-recovered pasa_asmbl_14707.p1, internal, 42492, 42579
-recovered pasa_asmbl_14707.p1, internal, 43105, 43193
Valid prediction for Augustus_model.g24900.t1
Valid prediction for snap_scaffold_15-snap.2849-T1
Valid prediction for snap_scaffold_15-snap.2859-T1
Valid prediction for snap_scaffold_15-snap.2823-T1
Valid prediction for snap_scaffold_15-snap.2844-T1
Valid prediction for snap_scaffold_15-snap.2851-T1
Valid prediction for snap_scaffold_15-snap.2866-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13976, rend_intergenic: 8092  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20019, rend_intergenic: 16423  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28705, rend_intergenic: 25624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33981, rend_intergenic: 32857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42822, rend_intergenic: 35549  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53266, rend_intergenic: 48525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57910, rend_intergenic: 55811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60088, rend_intergenic: 58186  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107150, rend_intergenic: 97664  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 226771
-exon list size: 357


building trellis

0.3    
0.6    
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1.1    
1.4    
1.7    
1.9    
2.2    
2.5    
2.8    
3.1    
3.3    
3.6    
3.9    
4.2    
4.5    
4.7    
5.0    
5.3    
5.6    
5.8    
6.1    
6.4    
6.7    
7.0    
7.2    
7.5    
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8.1    
8.4    
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9.2    
9.5    
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10.0    
10.3    
10.6    
10.9    
11.1    
11.4    
11.7    
12.0    
12.3    
12.5    
12.8    
13.1    
13.4    
13.6    
13.9    
14.2    
14.5    
14.8    
15.0    
15.3    
15.6    
15.9    
16.2    
16.4    
16.7    
17.0    
17.3    
17.5    
17.8    
18.1    
18.4    
18.7    
18.9    
19.2    
19.5    
19.8    
20.1    
20.3    
20.6    
20.9    
21.2    
21.4    
21.7    
22.0    
22.3    
22.6    
22.8    
23.1    
23.4    
23.7    
24.0    
24.2    
24.5    
24.8    
25.1    
25.3    
25.6    
25.9    
26.2    
26.5    
26.7    
27.0    
27.3    
27.6    
27.9    
28.1    
28.4    
28.7    
29.0    
29.2    
29.5    
29.8    
30.1    
30.4    
30.6    
30.9    
31.2    
31.5    
31.8    
32.0    
32.3    
32.6    
32.9    
33.1    
33.4    
33.7    
34.0    
34.3    
34.5    
34.8    
35.1    
35.4    
35.7    
35.9    
36.2    
36.5    
36.8    
37.0    
37.3    
37.6    
37.9    
38.2    
38.4    
38.7    
39.0    
39.3    
39.6    
39.8    
40.1    
40.4    
40.7    
40.9    
41.2    
41.5    
41.8    
42.1    
42.3    
42.6    
42.9    
43.2    
43.5    
43.7    
44.0    
44.3    
44.6    
44.8    
45.1    
45.4    
45.7    
46.0    
46.2    
46.5    
46.8    
47.1    
47.4    
47.6    
47.9    
48.2    
48.5    
48.7    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.3    
51.5    
51.8    
52.1    
52.4    
52.6    
52.9    
53.2    
53.5    
53.8    
54.0    
54.3    
54.6    
54.9    
55.2    
55.4    
55.7    
56.0    
56.3    
56.5    
56.8    
57.1    
57.4    
57.7    
57.9    
58.2    
58.5    
58.8    
59.1    
59.3    
59.6    
59.9    
60.2    
60.4    
60.7    
61.0    
61.3    
61.6    
61.8    
62.1    
62.4    
62.7    
63.0    
63.2    
63.5    
63.8    
64.1    
64.3    
64.6    
64.9    
65.2    
65.5    
65.7    
66.0    
66.3    
66.6    
66.9    
67.1    
67.4    
67.7    
68.0    
68.2    
68.5    
68.8    
69.1    
69.4    
69.6    
69.9    
70.2    
70.5    
70.8    
71.0    
71.3    
71.6    
71.9    
72.1    
72.4    
72.7    
73.0    
73.3    
73.5    
73.8    
74.1    
74.4    
74.7    
74.9    
75.2    
75.5    
75.8    
76.0    
76.3    
76.6    
76.9    
77.2    
77.4    
77.7    
78.0    
78.3    
78.6    
78.8    
79.1    
79.4    
79.7    
79.9    
80.2    
80.5    
80.8    
81.1    
81.3    
81.6    
81.9    
82.2    
82.5    
82.7    
83.0    
83.3    
83.6    
83.8    
84.1    
84.4    
84.7    
85.0    
85.2    
85.5    
85.8    
86.1    
86.4    
86.6    
86.9    
87.2    
87.5    
87.7    
88.0    
88.3    
88.6    
88.9    
89.1    
89.4    
89.7    
90.0    
90.3    
90.5    
90.8    
91.1    
91.4    
91.6    
91.9    
92.2    
92.5    
92.8    
93.0    
93.3    
93.6    
93.9    
94.2    
94.4    
94.7    
95.0    
95.3    
95.5    
95.8    
96.1    
96.4    
96.7    
96.9    
97.2    
97.5    
97.8    
98.1    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 13976, rend_intergenic: 8092  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20019, rend_intergenic: 16423  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28705, rend_intergenic: 25624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33981, rend_intergenic: 32857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42822, rend_intergenic: 35549  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53266, rend_intergenic: 48525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57910, rend_intergenic: 55811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60088, rend_intergenic: 58186  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107150, rend_intergenic: 97664  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support