-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_15851147-16018249

-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_5140-T1
Valid prediction for snap_scaffold_2-snap.3049-T1
Valid prediction for GlimmerHMM_glimmerT_5142-T1
Valid prediction for GlimmerHMM_glimmerT_5155-T1
Valid prediction for CodingQuarry_transcript_28782-T1
Valid prediction for snap_scaffold_2-snap.3047-T1
Valid prediction for snap_scaffold_2-snap.3067-T1
Valid prediction for GlimmerHMM_glimmerT_5153-T1
Couldn't classify 17767, 18072
Sorry, prediction pasa_asmbl_25082.p1 fails validation.
(CAC)	 CC	17767-18072	CG	AGC
Valid prediction for HiQ_model.g3484.t1
Valid prediction for Augustus_model.g3481.t1
Valid prediction for GlimmerHMM_glimmerT_5154-T1
Valid prediction for snap_scaffold_2-snap.3059-T1
Valid prediction for GlimmerHMM_glimmerT_5159-T1
Valid prediction for snap_scaffold_2-snap.3034-T1
Valid prediction for pasa_asmbl_25088.p1
Valid prediction for snap_scaffold_2-snap.3045-T1
Valid prediction for HiQ_model.g3478.t1
Valid prediction for Augustus_model.g3474.t1
Valid prediction for snap_scaffold_2-snap.3057-T1
Valid prediction for GlimmerHMM_glimmerT_5143-T1
Valid prediction for snap_scaffold_2-snap.3050-T1
Valid prediction for GlimmerHMM_glimmerT_5151-T1
Valid prediction for Augustus_model.g3471.t1
Valid prediction for snap_scaffold_2-snap.3051-T1
Valid prediction for GlimmerHMM_glimmerT_5152-T1
Valid prediction for Augustus_model.g3477.t1
Valid prediction for GlimmerHMM_glimmerT_5161-T1
Valid prediction for snap_scaffold_2-snap.3056-T1
Valid prediction for GlimmerHMM_glimmerT_5147-T1
Valid prediction for GlimmerHMM_glimmerT_5158-T1
Valid prediction for Augustus_model.g3483.t1
Couldn't classify 83196, 83216
Couldn't classify 87323, 87351
Sorry, prediction pasa_asmbl_25085.p1 fails validation.
(GCG)	 TG	83196-83216	GT	AGG
(CAA)	 AG	84128-84560	GT	GGG
(CCT)	 AG	84855-84939	GT	ATG
(GGA)	 AG	85092-85139	GT	AGG
(ATT)	 AG	85296-85386	GT	CAG
(GGC)	 AG	85547-85681	GT	GGG
(AGC)	 AG	85822-85927	GT	CAG
(TCA)	 AG	86024-86097	GT	CGG
(CTT)	 AG	86232-86392	GT	GGG
(ATT)	 AG	86566-86696	GT	CGG
(ATT)	 AG	86794-86971	GT	GGG
(GGT)	 AG	87076-87215	GT	AGG
(ATT)	 AG	87323-87351	GA	GTG
-recovered pasa_asmbl_25085.p1, internal, 84128, 84560
-recovered pasa_asmbl_25085.p1, internal, 84855, 84939
-recovered pasa_asmbl_25085.p1, internal, 85092, 85139
-recovered pasa_asmbl_25085.p1, internal, 85296, 85386
-recovered pasa_asmbl_25085.p1, internal, 85547, 85681
-recovered pasa_asmbl_25085.p1, internal, 85822, 85927
-recovered pasa_asmbl_25085.p1, internal, 86024, 86097
-recovered pasa_asmbl_25085.p1, internal, 86232, 86392
-recovered pasa_asmbl_25085.p1, internal, 86566, 86696
-recovered pasa_asmbl_25085.p1, internal, 86794, 86971
-recovered pasa_asmbl_25085.p1, internal, 87076, 87215
Valid prediction for snap_scaffold_2-snap.3062-T1
Valid prediction for snap_scaffold_2-snap.3036-T1
Couldn't classify 9658, 9923
Sorry, prediction pasa_asmbl_25078.p1 fails validation.
(TTT)	 TA	9658-9923	GT	AGG
(GTC)	 AG	12921-13114	GT	AAG
(TCC)	 AG	13237-13371	GT	AGG
(AAA)	 AG	13683-13757	GT	AGG
(GTT)	 AG	13888-13938	GT	TGG
(ACC)	 AG	15030-15242	GT	CGG
(GTC)	 AG	15455-15592	GT	TGG
(GTT)	 AG	15739-15883	GT	AGG
(GCG)	 AG	17622-17745	GA	AGG
-recovered pasa_asmbl_25078.p1, terminal, 17622, 17745
-recovered pasa_asmbl_25078.p1, internal, 12921, 13114
-recovered pasa_asmbl_25078.p1, internal, 13237, 13371
-recovered pasa_asmbl_25078.p1, internal, 13683, 13757
-recovered pasa_asmbl_25078.p1, internal, 13888, 13938
-recovered pasa_asmbl_25078.p1, internal, 15030, 15242
-recovered pasa_asmbl_25078.p1, internal, 15455, 15592
-recovered pasa_asmbl_25078.p1, internal, 15739, 15883
Valid prediction for Augustus_model.g3472.t1
Valid prediction for Augustus_model.g3476.t1
Valid prediction for GlimmerHMM_glimmerT_5144-T1
Valid prediction for snap_scaffold_2-snap.3053-T1
Valid prediction for snap_scaffold_2-snap.3042-T1
Valid prediction for snap_scaffold_2-snap.3044-T1
Valid prediction for snap_scaffold_2-snap.3069-T1
Valid prediction for snap_scaffold_2-snap.3061-T1
Valid prediction for snap_scaffold_2-snap.3055-T1
Valid prediction for snap_scaffold_2-snap.3043-T1
Valid prediction for HiQ_model.g3479.t1
Valid prediction for GlimmerHMM_glimmerT_5157-T1
Valid prediction for Augustus_model.g3475.t1
Valid prediction for GlimmerHMM_glimmerT_5138-T1
Valid prediction for GlimmerHMM_glimmerT_5149-T1
Valid prediction for snap_scaffold_2-snap.3048-T1
Valid prediction for snap_scaffold_2-snap.3039-T1
Couldn't classify 146780, 146873
Sorry, prediction pasa_asmbl_25092.p1 fails validation.
(CCC)	 CC	146780-146873	GT	GGG
(CTG)	 AG	147031-147200	GT	TGG
(GGA)	 AG	147313-147386	GT	CCG
(GGC)	 AG	147467-147716	GT	TGG
(AAT)	 AG	147843-148090	GT	AGG
(GCA)	 AG	148245-148392	GT	AGG
(ATC)	 AG	148474-148624	GT	CGG
(GTA)	 AG	148767-148843	GT	AGG
(TCC)	 AG	149154-149261	AT	AGA
-recovered pasa_asmbl_25092.p1, terminal, 149154, 149261
-recovered pasa_asmbl_25092.p1, internal, 147031, 147200
-recovered pasa_asmbl_25092.p1, internal, 147313, 147386
-recovered pasa_asmbl_25092.p1, internal, 147467, 147716
-recovered pasa_asmbl_25092.p1, internal, 147843, 148090
-recovered pasa_asmbl_25092.p1, internal, 148245, 148392
-recovered pasa_asmbl_25092.p1, internal, 148474, 148624
-recovered pasa_asmbl_25092.p1, internal, 148767, 148843
Valid prediction for Augustus_model.g3480.t1
Valid prediction for snap_scaffold_2-snap.3054-T1
Valid prediction for snap_scaffold_2-snap.3041-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_2-snap.3063-T1
Valid prediction for GlimmerHMM_glimmerT_5156-T1
Valid prediction for snap_scaffold_2-snap.3060-T1
Valid prediction for snap_scaffold_2-snap.3046-T1
Valid prediction for snap_scaffold_2-snap.3040-T1
Valid prediction for snap_scaffold_2-snap.3064-T1
Valid prediction for Augustus_model.g3482.t1
Valid prediction for snap_scaffold_2-snap.3066-T1
Valid prediction for CodingQuarry_transcript_28781-T1
Couldn't classify 145831, 145910
Sorry, prediction pasa_asmbl_23932.p1 fails validation.
(ATG)	 AA	145052-145111	GT	TGG
(AAG)	 AG	145204-145300	GT	CGG
(GTG)	 AG	145445-145534	GT	TGG
(ATG)	 AG	145633-145716	GT	CGG
(AGC)	 AG	145831-145910	GT	CAG
-recovered pasa_asmbl_23932.p1, initial, 145052, 145111
add_exon() Sorry, pasa_asmbl_23932.p1 145633-145716-initial-1 is invalid.
-recovered pasa_asmbl_23932.p1, initial, 145633, 145716
-recovered pasa_asmbl_23932.p1, internal, 145204, 145300
-recovered pasa_asmbl_23932.p1, internal, 145445, 145534
-recovered pasa_asmbl_23932.p1, internal, 145633, 145716
-recovered pasa_asmbl_23932.p1, internal, 145831, 145910
Valid prediction for GlimmerHMM_glimmerT_5139-T1
Valid prediction for snap_scaffold_2-snap.3032-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_5150-T1
Valid prediction for GlimmerHMM_glimmerT_5141-T1
Valid prediction for GlimmerHMM_glimmerT_5160-T1
Valid prediction for snap_scaffold_2-snap.3058-T1
Valid prediction for snap_scaffold_2-snap.3070-T1
Valid prediction for snap_scaffold_2-snap.3052-T1
Valid prediction for snap_scaffold_2-snap.3068-T1
Valid prediction for GlimmerHMM_glimmerT_5148-T1
Valid prediction for HiQ_model.g3473.t1
Valid prediction for snap_scaffold_2-snap.3065-T1
Valid prediction for snap_scaffold_2-snap.3037-T1
Valid prediction for GlimmerHMM_glimmerT_5163-T1
Valid prediction for snap_scaffold_2-snap.3033-T1
Valid prediction for GlimmerHMM_glimmerT_5146-T1
Valid prediction for snap_scaffold_2-snap.3038-T1
Valid prediction for GlimmerHMM_glimmerT_5145-T1
Valid prediction for snap_scaffold_2-snap.3035-T1
Valid prediction for GlimmerHMM_glimmerT_5137-T1
Valid prediction for GlimmerHMM_glimmerT_5162-T1
Valid prediction for Augustus_model.g3485.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17102, rend_intergenic: 11906  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29496, rend_intergenic: 27095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30882, rend_intergenic: 30117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108172, rend_intergenic: 104267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118762, rend_intergenic: 117503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123946, rend_intergenic: 123323  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149508, rend_intergenic: 140120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 167103
-exon list size: 341


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.7    
2.0    
2.3    
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2.9    
3.2    
3.5    
3.8    
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4.4    
4.7    
5.0    
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5.5    
5.8    
6.1    
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6.7    
7.0    
7.3    
7.6    
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8.5    
8.7    
9.0    
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9.9    
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10.8    
11.1    
11.4    
11.7    
12.0    
12.2    
12.5    
12.8    
13.1    
13.4    
13.7    
14.0    
14.3    
14.6    
14.9    
15.2    
15.5    
15.7    
16.0    
16.3    
16.6    
16.9    
17.2    
17.5    
17.8    
18.1    
18.4    
18.7    
19.0    
19.2    
19.5    
19.8    
20.1    
20.4    
20.7    
21.0    
21.3    
21.6    
21.9    
22.2    
22.4    
22.7    
23.0    
23.3    
23.6    
23.9    
24.2    
24.5    
24.8    
25.1    
25.4    
25.7    
25.9    
26.2    
26.5    
26.8    
27.1    
27.4    
27.7    
28.0    
28.3    
28.6    
28.9    
29.2    
29.4    
29.7    
30.0    
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    
35.6    
35.9    
36.2    
36.4    
36.7    
37.0    
37.3    
37.6    
37.9    
38.2    
38.5    
38.8    
39.1    
39.4    
39.7    
39.9    
40.2    
40.5    
40.8    
41.1    
41.4    
41.7    
42.0    
42.3    
42.6    
42.9    
43.1    
43.4    
43.7    
44.0    
44.3    
44.6    
44.9    
45.2    
45.5    
45.8    
46.1    
46.4    
46.6    
46.9    
47.2    
47.5    
47.8    
48.1    
48.4    
48.7    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.3    
51.6    
51.9    
52.2    
52.5    
52.8    
53.1    
53.4    
53.6    
53.9    
54.2    
54.5    
54.8    
55.1    
55.4    
55.7    
56.0    
56.3    
56.6    
56.9    
57.1    
57.4    
57.7    
58.0    
58.3    
58.6    
58.9    
59.2    
59.5    
59.8    
60.1    
60.3    
60.6    
60.9    
61.2    
61.5    
61.8    
62.1    
62.4    
62.7    
63.0    
63.3    
63.6    
63.8    
64.1    
64.4    
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    
70.0    
70.3    
70.6    
70.8    
71.1    
71.4    
71.7    
72.0    
72.3    
72.6    
72.9    
73.2    
73.5    
73.8    
74.1    
74.3    
74.6    
74.9    
75.2    
75.5    
75.8    
76.1    
76.4    
76.7    
77.0    
77.3    
77.6    
77.8    
78.1    
78.4    
78.7    
79.0    
79.3    
79.6    
79.9    
80.2    
80.5    
80.8    
81.0    
81.3    
81.6    
81.9    
82.2    
82.5    
82.8    
83.1    
83.4    
83.7    
84.0    
84.3    
84.5    
84.8    
85.1    
85.4    
85.7    
86.0    
86.3    
86.6    
86.9    
87.2    
87.5    
87.8    
88.0    
88.3    
88.6    
88.9    
89.2    
89.5    
89.8    
90.1    
90.4    
90.7    
91.0    
91.3    
91.5    
91.8    
92.1    
92.4    
92.7    
93.0    
93.3    
93.6    
93.9    
94.2    
94.5    
94.8    
95.0    
95.3    
95.6    
95.9    
96.2    
96.5    
96.8    
97.1    
97.4    
97.7    
98.0    
98.3    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 17102, rend_intergenic: 11906  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29496, rend_intergenic: 27095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30882, rend_intergenic: 30117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108172, rend_intergenic: 104267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118762, rend_intergenic: 117503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123946, rend_intergenic: 123323  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149508, rend_intergenic: 140120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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