-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_19394492-19747749

-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 snap_scaffold_2-snap.3805-T1
Valid prediction for snap_scaffold_2-snap.3822-T1
Valid prediction for snap_scaffold_2-snap.3837-T1
Valid prediction for GlimmerHMM_glimmerT_5703-T1
Valid prediction for Augustus_model.g3787.t1
Valid prediction for Augustus_model.g3789.t1
Valid prediction for snap_scaffold_2-snap.3821-T1
Valid prediction for snap_scaffold_2-snap.3834-T1
Valid prediction for Augustus_model.g3791.t1
Valid prediction for snap_scaffold_2-snap.3810-T1
Valid prediction for snap_scaffold_2-snap.3798-T1
Valid prediction for snap_scaffold_2-snap.3816-T1
Valid prediction for snap_scaffold_2-snap.3818-T1
Couldn't classify 290363, 291502
Sorry, prediction pasa_asmbl_25284.p1 fails validation.
(TTG)	 TG	290363-291502	AG	AGA
Valid prediction for snap_scaffold_2-snap.3826-T1
Valid prediction for GlimmerHMM_glimmerT_5672-T1
Valid prediction for snap_scaffold_2-snap.3793-T1
Valid prediction for GlimmerHMM_glimmerT_5684-T1
Valid prediction for GlimmerHMM_glimmerT_5694-T1
Valid prediction for GlimmerHMM_glimmerT_5701-T1
Valid prediction for GlimmerHMM_glimmerT_5680-T1
Valid prediction for snap_scaffold_2-snap.3825-T1
Valid prediction for snap_scaffold_2-snap.3807-T1
Valid prediction for GlimmerHMM_glimmerT_5687-T1
Valid prediction for GlimmerHMM_glimmerT_5685-T1
Valid prediction for GlimmerHMM_glimmerT_5678-T1
Valid prediction for snap_scaffold_2-snap.3813-T1
Valid prediction for GlimmerHMM_glimmerT_5682-T1
Valid prediction for Augustus_model.g3795.t1
Valid prediction for GlimmerHMM_glimmerT_5699-T1
Valid prediction for GlimmerHMM_glimmerT_5676-T1
Valid prediction for GlimmerHMM_glimmerT_5683-T1
Valid prediction for snap_scaffold_2-snap.3801-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.3803-T1
Valid prediction for GlimmerHMM_glimmerT_5698-T1
Valid prediction for GlimmerHMM_glimmerT_5679-T1
Valid prediction for snap_scaffold_2-snap.3819-T1
Valid prediction for snap_scaffold_2-snap.3811-T1
Valid prediction for snap_scaffold_2-snap.3823-T1
Valid prediction for snap_scaffold_2-snap.3802-T1
Valid prediction for snap_scaffold_2-snap.3809-T1
Valid prediction for GlimmerHMM_glimmerT_5690-T1
Valid prediction for snap_scaffold_2-snap.3827-T1
Valid prediction for snap_scaffold_2-snap.3838-T1
Valid prediction for GlimmerHMM_glimmerT_5692-T1
Valid prediction for snap_scaffold_2-snap.3795-T1
Valid prediction for snap_scaffold_2-snap.3839-T1
Valid prediction for Augustus_model.g3794.t1
Valid prediction for Augustus_model.g3792.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.3824-T1
Valid prediction for GlimmerHMM_glimmerT_5704-T1
Valid prediction for snap_scaffold_2-snap.3794-T1
Valid prediction for snap_scaffold_2-snap.3820-T1
Valid prediction for snap_scaffold_2-snap.3800-T1
Valid prediction for snap_scaffold_2-snap.3828-T1
Valid prediction for snap_scaffold_2-snap.3831-T1
Couldn't classify 198725, 199048
Couldn't classify 199410, 199541
Sorry, prediction pasa_asmbl_23873.p1 fails validation.
(GAC)	 TG	198725-199048	GT	GGG
(CTA)	 AG	199410-199541	TA	ACT
Couldn't classify 204420, 204450
Sorry, prediction pasa_asmbl_23872.p1 fails validation.
(GAA)	 TG	204420-204450	GT	AGG
(GAA)	 AG	204688-204848	GT	AGG
(TTG)	 AG	205085-205268	GT	AGG
(GTC)	 AG	205523-207387	GG	GAG
-recovered pasa_asmbl_23872.p1, terminal, 205523, 207387
-recovered pasa_asmbl_23872.p1, internal, 204688, 204848
-recovered pasa_asmbl_23872.p1, internal, 205085, 205268
Valid prediction for snap_scaffold_2-snap.3812-T1
Valid prediction for Augustus_model.g3788.t1
Valid prediction for snap_scaffold_2-snap.3835-T1
Valid prediction for snap_scaffold_2-snap.3836-T1
Valid prediction for GlimmerHMM_glimmerT_5697-T1
Valid prediction for snap_scaffold_2-snap.3832-T1
Valid prediction for Augustus_model.g3790.t1
Valid prediction for GlimmerHMM_glimmerT_5691-T1
Valid prediction for GlimmerHMM_glimmerT_5693-T1
Valid prediction for GlimmerHMM_glimmerT_5673-T1
Couldn't classify 350784, 350933
Sorry, prediction pasa_asmbl_23869.p1 fails validation.
(ATG)	 CC	349099-349293	GT	AGG
(GTT)	 AG	350784-350933	CG	CAC
-recovered pasa_asmbl_23869.p1, initial, 349099, 349293
Valid prediction for snap_scaffold_2-snap.3815-T1
Valid prediction for GlimmerHMM_glimmerT_5702-T1
Valid prediction for snap_scaffold_2-snap.3817-T1
Valid prediction for GlimmerHMM_glimmerT_5695-T1
Valid prediction for snap_scaffold_2-snap.3804-T1
Valid prediction for snap_scaffold_2-snap.3830-T1
Valid prediction for snap_scaffold_2-snap.3814-T1
Valid prediction for snap_scaffold_2-snap.3796-T1
Valid prediction for GlimmerHMM_glimmerT_5689-T1
Valid prediction for snap_scaffold_2-snap.3808-T1
Valid prediction for GlimmerHMM_glimmerT_5674-T1
Valid prediction for GlimmerHMM_glimmerT_5677-T1
Valid prediction for GlimmerHMM_glimmerT_5700-T1
Valid prediction for snap_scaffold_2-snap.3829-T1
Valid prediction for snap_scaffold_2-snap.3799-T1
Valid prediction for GlimmerHMM_glimmerT_5688-T1
Valid prediction for snap_scaffold_2-snap.3806-T1
Valid prediction for GlimmerHMM_glimmerT_5681-T1
Valid prediction for GlimmerHMM_glimmerT_5675-T1
Valid prediction for snap_scaffold_2-snap.3797-T1
Valid prediction for snap_scaffold_2-snap.3833-T1
Valid prediction for Augustus_model.g3793.t1
Valid prediction for GlimmerHMM_glimmerT_5686-T1
Valid prediction for GlimmerHMM_glimmerT_5696-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 26796, rend_intergenic: 12371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32897, rend_intergenic: 27481  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37812, rend_intergenic: 33053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41282, rend_intergenic: 37815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53925, rend_intergenic: 49219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59195, rend_intergenic: 57761  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63309, rend_intergenic: 61724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65171, rend_intergenic: 63369  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67411, rend_intergenic: 65725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75961, rend_intergenic: 68348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90163, rend_intergenic: 79933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92882, rend_intergenic: 90330  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94535, rend_intergenic: 93748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95691, rend_intergenic: 95179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97442, rend_intergenic: 95843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110690, rend_intergenic: 104383  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123016, rend_intergenic: 113122  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 73204, rend_intergenic: 73201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 353258
-exon list size: 286


building trellis

0.3    
0.7    
1.0    
1.4    
1.7    
2.1    
2.4    
2.8    
3.1    
3.5    
3.8    
4.2    
4.5    
4.9    
5.2    
5.6    
5.9    
6.2    
6.6    
6.9    
7.3    
7.6    
8.0    
8.3    
8.7    
9.0    
9.4    
9.7    
10.1    
10.4    
10.8    
11.1    
11.5    
11.8    
12.2    
12.5    
12.8    
13.2    
13.5    
13.9    
14.2    
14.6    
14.9    
15.3    
15.6    
16.0    
16.3    
16.7    
17.0    
17.4    
17.7    
18.1    
18.4    
18.8    
19.1    
19.4    
19.8    
20.1    
20.5    
20.8    
21.2    
21.5    
21.9    
22.2    
22.6    
22.9    
23.3    
23.6    
24.0    
24.3    
24.7    
25.0    
25.3    
25.7    
26.0    
26.4    
26.7    
27.1    
27.4    
27.8    
28.1    
28.5    
28.8    
29.2    
29.5    
29.9    
30.2    
30.6    
30.9    
31.2    
31.6    
31.9    
32.3    
32.6    
33.0    
33.3    
33.7    
34.0    
34.4    
34.7    
35.1    
35.4    
35.8    
36.1    
36.5    
36.8    
37.2    
37.5    
37.8    
38.2    
38.5    
38.9    
39.2    
39.6    
39.9    
40.3    
40.6    
41.0    
41.3    
41.7    
42.0    
42.4    
42.7    
43.1    
43.4    
43.8    
44.1    
44.4    
44.8    
45.1    
45.5    
45.8    
46.2    
46.5    
46.9    
47.2    
47.6    
47.9    
48.3    
48.6    
49.0    
49.3    
49.7    
50.0    
50.3    
50.7    
51.0    
51.4    
51.7    
52.1    
52.4    
52.8    
53.1    
53.5    
53.8    
54.2    
54.5    
54.9    
55.2    
55.6    
55.9    
56.2    
56.6    
56.9    
57.3    
57.6    
58.0    
58.3    
58.7    
59.0    
59.4    
59.7    
60.1    
60.4    
60.8    
61.1    
61.5    
61.8    
62.2    
62.5    
62.8    
63.2    
63.5    
63.9    
64.2    
64.6    
64.9    
65.3    
65.6    
66.0    
66.3    
66.7    
67.0    
67.4    
67.7    
68.1    
68.4    
68.8    
69.1    
69.4    
69.8    
70.1    
70.5    
70.8    
71.2    
71.5    
71.9    
72.2    
72.6    
72.9    
73.3    
73.6    
74.0    
74.3    
74.7    
75.0    
75.3    
75.7    
76.0    
76.4    
76.7    
77.1    
77.4    
77.8    
78.1    
78.5    
78.8    
79.2    
79.5    
79.9    
80.2    
80.6    
80.9    
81.2    
81.6    
81.9    
82.3    
82.6    
83.0    
83.3    
83.7    
84.0    
84.4    
84.7    
85.1    
85.4    
85.8    
86.1    
86.5    
86.8    
87.2    
87.5    
87.8    
88.2    
88.5    
88.9    
89.2    
89.6    
89.9    
90.3    
90.6    
91.0    
91.3    
91.7    
92.0    
92.4    
92.7    
93.1    
93.4    
93.8    
94.1    
94.4    
94.8    
95.1    
95.5    
95.8    
96.2    
96.5    
96.9    
97.2    
97.6    
97.9    
98.3    
98.6    
99.0    
99.3    
99.7    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 26796, rend_intergenic: 12371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32897, rend_intergenic: 27481  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37812, rend_intergenic: 33053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41282, rend_intergenic: 37815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53925, rend_intergenic: 49219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59195, rend_intergenic: 57761  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63309, rend_intergenic: 61724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65171, rend_intergenic: 63369  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67411, rend_intergenic: 65725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75961, rend_intergenic: 68348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90163, rend_intergenic: 79933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92882, rend_intergenic: 90330  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94535, rend_intergenic: 93748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95691, rend_intergenic: 95179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97442, rend_intergenic: 95843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110690, rend_intergenic: 104383  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123016, rend_intergenic: 113122  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 73204, rend_intergenic: 73201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support