-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_19398811-19696034

-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_5817-T1
Valid prediction for GlimmerHMM_glimmerT_5809-T1
Valid prediction for Augustus_model.g3893.t1
Valid prediction for GeneMark_model.9467_t
Valid prediction for Augustus_model.g3895.t1
Valid prediction for GeneMark_model.9484_t
Valid prediction for snap_scaffold_2-snap.3854-T1
Valid prediction for GlimmerHMM_glimmerT_5805-T1
Valid prediction for GlimmerHMM_glimmerT_5798-T1
Valid prediction for GlimmerHMM_glimmerT_5804-T1
Valid prediction for snap_scaffold_2-snap.3851-T1
Valid prediction for GeneMark_model.9485_t
Valid prediction for snap_scaffold_2-snap.3867-T1
Valid prediction for GeneMark_model.9489_t
Valid prediction for Augustus_model.g3899.t1
Valid prediction for snap_scaffold_2-snap.3876-T1
Valid prediction for GeneMark_model.9465_t
Valid prediction for GlimmerHMM_glimmerT_5795-T1
Valid prediction for GlimmerHMM_glimmerT_5803-T1
Valid prediction for GeneMark_model.9458_t
Valid prediction for snap_scaffold_2-snap.3871-T1
Valid prediction for GeneMark_model.9470_t
Valid prediction for snap_scaffold_2-snap.3845-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.3850-T1
Valid prediction for GlimmerHMM_glimmerT_5819-T1
Valid prediction for GlimmerHMM_glimmerT_5815-T1
Valid prediction for snap_scaffold_2-snap.3846-T1
Valid prediction for snap_scaffold_2-snap.3862-T1
Valid prediction for GlimmerHMM_glimmerT_5806-T1
Valid prediction for snap_scaffold_2-snap.3860-T1
Valid prediction for GlimmerHMM_glimmerT_5811-T1
Valid prediction for GlimmerHMM_glimmerT_5800-T1
Valid prediction for GeneMark_model.9461_t
Valid prediction for GeneMark_model.9490_t
Valid prediction for snap_scaffold_2-snap.3869-T1
Valid prediction for Augustus_model.g3891.t1
Valid prediction for GeneMark_model.9463_t
Valid prediction for GeneMark_model.9504_t
Valid prediction for snap_scaffold_2-snap.3865-T1
Valid prediction for snap_scaffold_2-snap.3863-T1
Valid prediction for snap_scaffold_2-snap.3855-T1
Valid prediction for GeneMark_model.9460_t
Valid prediction for GeneMark_model.9499_t
Valid prediction for snap_scaffold_2-snap.3857-T1
Valid prediction for GeneMark_model.9475_t
Valid prediction for snap_scaffold_2-snap.3866-T1
Valid prediction for snap_scaffold_2-snap.3879-T1
Valid prediction for GeneMark_model.9471_t
Valid prediction for GeneMark_model.9473_t
Valid prediction for GeneMark_model.9479_t
Valid prediction for snap_scaffold_2-snap.3840-T1
Valid prediction for GeneMark_model.9478_t
Couldn't classify 286044, 287183
Sorry, prediction pasa_asmbl_25317.p1 fails validation.
(TTG)	 TG	286044-287183	AG	AGA
Valid prediction for snap_scaffold_2-snap.3847-T1
Valid prediction for GeneMark_model.9481_t
Valid prediction for GlimmerHMM_glimmerT_5816-T1
Valid prediction for GeneMark_model.9468_t
Valid prediction for Augustus_model.g3898.t1
Valid prediction for Augustus_model.g3896.t1
Valid prediction for GeneMark_model.9487_t
Valid prediction for snap_scaffold_2-snap.3881-T1
Valid prediction for snap_scaffold_2-snap.3870-T1
Valid prediction for snap_scaffold_2-snap.3838-T1
Valid prediction for snap_scaffold_2-snap.3853-T1
Valid prediction for GeneMark_model.9469_t
Valid prediction for GlimmerHMM_glimmerT_5797-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 GeneMark_model.9494_t
Valid prediction for snap_scaffold_2-snap.3849-T1
Valid prediction for snap_scaffold_2-snap.3856-T1
Valid prediction for GlimmerHMM_glimmerT_5801-T1
Valid prediction for snap_scaffold_2-snap.3839-T1
Valid prediction for snap_scaffold_2-snap.3858-T1
Valid prediction for GlimmerHMM_glimmerT_5794-T1
Couldn't classify 147010, 147333
Couldn't classify 147695, 147826
Sorry, prediction pasa_asmbl_23891.p1 fails validation.
(GAC)	 TG	147010-147333	GT	GGG
(CTA)	 AG	147695-147826	TA	ACT
Valid prediction for GeneMark_model.9477_t
Valid prediction for GlimmerHMM_glimmerT_5812-T1
Valid prediction for Augustus_model.g3889.t1
Valid prediction for snap_scaffold_2-snap.3875-T1
Valid prediction for GeneMark_model.9459_t
Valid prediction for snap_scaffold_2-snap.3844-T1
Valid prediction for snap_scaffold_2-snap.3872-T1
Couldn't classify 152705, 152735
Sorry, prediction pasa_asmbl_23890.p1 fails validation.
(GAA)	 TG	152705-152735	GT	AGG
(GAA)	 AG	152973-153133	GT	AGG
(TTG)	 AG	153370-153553	GT	AGG
(GTC)	 AG	153808-155672	GG	GAG
-recovered pasa_asmbl_23890.p1, terminal, 153808, 155672
-recovered pasa_asmbl_23890.p1, internal, 152973, 153133
-recovered pasa_asmbl_23890.p1, internal, 153370, 153553
Valid prediction for snap_scaffold_2-snap.3878-T1
Valid prediction for snap_scaffold_2-snap.3873-T1
Valid prediction for GeneMark_model.9497_t
Valid prediction for GlimmerHMM_glimmerT_5792-T1
Valid prediction for snap_scaffold_2-snap.3880-T1
Valid prediction for Augustus_model.g3892.t1
Valid prediction for GeneMark_model.9493_t
Valid prediction for snap_scaffold_2-snap.3868-T1
Valid prediction for Augustus_model.g3890.t1
Valid prediction for GlimmerHMM_glimmerT_5810-T1
Valid prediction for GeneMark_model.9474_t
Valid prediction for GlimmerHMM_glimmerT_5818-T1
Valid prediction for snap_scaffold_2-snap.3861-T1
Valid prediction for HiQ_model.g3894.t1
Valid prediction for GeneMark_model.9462_t
Valid prediction for snap_scaffold_2-snap.3841-T1
Valid prediction for GlimmerHMM_glimmerT_5808-T1
Valid prediction for GeneMark_model.9486_t
Valid prediction for GeneMark_model.9501_t
Valid prediction for snap_scaffold_2-snap.3852-T1
Valid prediction for snap_scaffold_2-snap.3859-T1
Valid prediction for GlimmerHMM_glimmerT_5796-T1
Valid prediction for GeneMark_model.9472_t
Valid prediction for GeneMark_model.9496_t
Valid prediction for GeneMark_model.9464_t
Valid prediction for GeneMark_model.9498_t
Valid prediction for GlimmerHMM_glimmerT_5793-T1
Valid prediction for GlimmerHMM_glimmerT_5799-T1
Valid prediction for snap_scaffold_2-snap.3843-T1
Valid prediction for snap_scaffold_2-snap.3864-T1
Valid prediction for Augustus_model.g3897.t1
Valid prediction for GeneMark_model.9500_t
Valid prediction for GlimmerHMM_glimmerT_5814-T1
Valid prediction for GeneMark_model.9492_t
Valid prediction for snap_scaffold_2-snap.3848-T1
Valid prediction for snap_scaffold_2-snap.3842-T1
Valid prediction for GeneMark_model.9476_t
Valid prediction for snap_scaffold_2-snap.3877-T1
Valid prediction for GeneMark_model.9482_t
Valid prediction for GeneMark_model.9503_t
Valid prediction for GeneMark_model.9495_t
Valid prediction for GlimmerHMM_glimmerT_5802-T1
Valid prediction for GeneMark_model.9466_t
Valid prediction for snap_scaffold_2-snap.3874-T1
Valid prediction for GeneMark_model.9488_t
Valid prediction for GeneMark_model.9502_t
Valid prediction for GlimmerHMM_glimmerT_5807-T1
Valid prediction for GlimmerHMM_glimmerT_5813-T1
Valid prediction for GeneMark_model.9480_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 68885, rend_intergenic: 68882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22477, rend_intergenic: 8052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28578, rend_intergenic: 23162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33112, rend_intergenic: 28734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49606, rend_intergenic: 44900  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54876, rend_intergenic: 53442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60720, rend_intergenic: 59850  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63092, rend_intergenic: 61406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71642, rend_intergenic: 64029  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75569, rend_intergenic: 75496  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85844, rend_intergenic: 75614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88789, rend_intergenic: 86011  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90216, rend_intergenic: 89429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91372, rend_intergenic: 90860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93123, rend_intergenic: 91524  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106371, rend_intergenic: 100064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118697, rend_intergenic: 110353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 297224
-exon list size: 647


building trellis

0.2    
0.3    
0.5    
0.6    
0.8    
0.9    
1.1    
1.2    
1.4    
1.5    
1.7    
1.8    
2.0    
2.2    
2.3    
2.5    
2.6    
2.8    
2.9    
3.1    
3.2    
3.4    
3.5    
3.7    
3.9    
4.0    
4.2    
4.3    
4.5    
4.6    
4.8    
4.9    
5.1    
5.2    
5.4    
5.5    
5.7    
5.9    
6.0    
6.2    
6.3    
6.5    
6.6    
6.8    
6.9    
7.1    
7.2    
7.4    
7.6    
7.7    
7.9    
8.0    
8.2    
8.3    
8.5    
8.6    
8.8    
8.9    
9.1    
9.2    
9.4    
9.6    
9.7    
9.9    
10.0    
10.2    
10.3    
10.5    
10.6    
10.8    
10.9    
11.1    
11.2    
11.4    
11.6    
11.7    
11.9    
12.0    
12.2    
12.3    
12.5    
12.6    
12.8    
12.9    
13.1    
13.3    
13.4    
13.6    
13.7    
13.9    
14.0    
14.2    
14.3    
14.5    
14.6    
14.8    
14.9    
15.1    
15.3    
15.4    
15.6    
15.7    
15.9    
16.0    
16.2    
16.3    
16.5    
16.6    
16.8    
16.9    
17.1    
17.3    
17.4    
17.6    
17.7    
17.9    
18.0    
18.2    
18.3    
18.5    
18.6    
18.8    
19.0    
19.1    
19.3    
19.4    
19.6    
19.7    
19.9    
20.0    
20.2    
20.3    
20.5    
20.6    
20.8    
21.0    
21.1    
21.3    
21.4    
21.6    
21.7    
21.9    
22.0    
22.2    
22.3    
22.5    
22.7    
22.8    
23.0    
23.1    
23.3    
23.4    
23.6    
23.7    
23.9    
24.0    
24.2    
24.3    
24.5    
24.7    
24.8    
25.0    
25.1    
25.3    
25.4    
25.6    
25.7    
25.9    
26.0    
26.2    
26.3    
26.5    
26.7    
26.8    
27.0    
27.1    
27.3    
27.4    
27.6    
27.7    
27.9    
28.0    
28.2    
28.4    
28.5    
28.7    
28.8    
29.0    
29.1    
29.3    
29.4    
29.6    
29.7    
29.9    
30.0    
30.2    
30.4    
30.5    
30.7    
30.8    
31.0    
31.1    
31.3    
31.4    
31.6    
31.7    
31.9    
32.0    
32.2    
32.4    
32.5    
32.7    
32.8    
33.0    
33.1    
33.3    
33.4    
33.6    
33.7    
33.9    
34.1    
34.2    
34.4    
34.5    
34.7    
34.8    
35.0    
35.1    
35.3    
35.4    
35.6    
35.7    
35.9    
36.1    
36.2    
36.4    
36.5    
36.7    
36.8    
37.0    
37.1    
37.3    
37.4    
37.6    
37.8    
37.9    
38.1    
38.2    
38.4    
38.5    
38.7    
38.8    
39.0    
39.1    
39.3    
39.4    
39.6    
39.8    
39.9    
40.1    
40.2    
40.4    
40.5    
40.7    
40.8    
41.0    
41.1    
41.3    
41.4    
41.6    
41.8    
41.9    
42.1    
42.2    
42.4    
42.5    
42.7    
42.8    
43.0    
43.1    
43.3    
43.5    
43.6    
43.8    
43.9    
44.1    
44.2    
44.4    
44.5    
44.7    
44.8    
45.0    
45.1    
45.3    
45.5    
45.6    
45.8    
45.9    
46.1    
46.2    
46.4    
46.5    
46.7    
46.8    
47.0    
47.1    
47.3    
47.5    
47.6    
47.8    
47.9    
48.1    
48.2    
48.4    
48.5    
48.7    
48.8    
49.0    
49.2    
49.3    
49.5    
49.6    
49.8    
49.9    
50.1    
50.2    
50.4    
50.5    
50.7    
50.8    
51.0    
51.2    
51.3    
51.5    
51.6    
51.8    
51.9    
52.1    
52.2    
52.4    
52.5    
52.7    
52.9    
53.0    
53.2    
53.3    
53.5    
53.6    
53.8    
53.9    
54.1    
54.2    
54.4    
54.5    
54.7    
54.9    
55.0    
55.2    
55.3    
55.5    
55.6    
55.8    
55.9    
56.1    
56.2    
56.4    
56.5    
56.7    
56.9    
57.0    
57.2    
57.3    
57.5    
57.6    
57.8    
57.9    
58.1    
58.2    
58.4    
58.6    
58.7    
58.9    
59.0    
59.2    
59.3    
59.5    
59.6    
59.8    
59.9    
60.1    
60.2    
60.4    
60.6    
60.7    
60.9    
61.0    
61.2    
61.3    
61.5    
61.6    
61.8    
61.9    
62.1    
62.2    
62.4    
62.6    
62.7    
62.9    
63.0    
63.2    
63.3    
63.5    
63.6    
63.8    
63.9    
64.1    
64.3    
64.4    
64.6    
64.7    
64.9    
65.0    
65.2    
65.3    
65.5    
65.6    
65.8    
65.9    
66.1    
66.3    
66.4    
66.6    
66.7    
66.9    
67.0    
67.2    
67.3    
67.5    
67.6    
67.8    
68.0    
68.1    
68.3    
68.4    
68.6    
68.7    
68.9    
69.0    
69.2    
69.3    
69.5    
69.6    
69.8    
70.0    
70.1    
70.3    
70.4    
70.6    
70.7    
70.9    
71.0    
71.2    
71.3    
71.5    
71.6    
71.8    
72.0    
72.1    
72.3    
72.4    
72.6    
72.7    
72.9    
73.0    
73.2    
73.3    
73.5    
73.7    
73.8    
74.0    
74.1    
74.3    
74.4    
74.6    
74.7    
74.9    
75.0    
75.2    
75.3    
75.5    
75.7    
75.8    
76.0    
76.1    
76.3    
76.4    
76.6    
76.7    
76.9    
77.0    
77.2    
77.3    
77.5    
77.7    
77.8    
78.0    
78.1    
78.3    
78.4    
78.6    
78.7    
78.9    
79.0    
79.2    
79.4    
79.5    
79.7    
79.8    
80.0    
80.1    
80.3    
80.4    
80.6    
80.7    
80.9    
81.0    
81.2    
81.4    
81.5    
81.7    
81.8    
82.0    
82.1    
82.3    
82.4    
82.6    
82.7    
82.9    
83.1    
83.2    
83.4    
83.5    
83.7    
83.8    
84.0    
84.1    
84.3    
84.4    
84.6    
84.7    
84.9    
85.1    
85.2    
85.4    
85.5    
85.7    
85.8    
86.0    
86.1    
86.3    
86.4    
86.6    
86.7    
86.9    
87.1    
87.2    
87.4    
87.5    
87.7    
87.8    
88.0    
88.1    
88.3    
88.4    
88.6    
88.8    
88.9    
89.1    
89.2    
89.4    
89.5    
89.7    
89.8    
90.0    
90.1    
90.3    
90.4    
90.6    
90.8    
90.9    
91.1    
91.2    
91.4    
91.5    
91.7    
91.8    
92.0    
92.1    
92.3    
92.4    
92.6    
92.8    
92.9    
93.1    
93.2    
93.4    
93.5    
93.7    
93.8    
94.0    
94.1    
94.3    
94.5    
94.6    
94.8    
94.9    
95.1    
95.2    
95.4    
95.5    
95.7    
95.8    
96.0    
96.1    
96.3    
96.5    
96.6    
96.8    
96.9    
97.1    
97.2    
97.4    
97.5    
97.7    
97.8    
98.0    
98.2    
98.3    
98.5    
98.6    
98.8    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 38 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 68885, rend_intergenic: 68882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22477, rend_intergenic: 8052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28578, rend_intergenic: 23162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33112, rend_intergenic: 28734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49606, rend_intergenic: 44900  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54876, rend_intergenic: 53442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60720, rend_intergenic: 59850  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63092, rend_intergenic: 61406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71642, rend_intergenic: 64029  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75569, rend_intergenic: 75496  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85844, rend_intergenic: 75614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88789, rend_intergenic: 86011  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90216, rend_intergenic: 89429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91372, rend_intergenic: 90860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93123, rend_intergenic: 91524  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106371, rend_intergenic: 100064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118697, rend_intergenic: 110353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 12849
-exon list size: 28


building trellis

3.3    
6.7    
10.0    
13.3    
16.7    
20.0    
23.3    
26.7    
30.0    
33.3    
36.7    
40.0    
43.3    
46.7    
50.0    
53.3    
56.7    
60.0    
63.3    
66.7    
70.0    
73.3    
76.7    
80.0    
83.3    
86.7    
90.0    
93.3    
96.7    
-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 287184 - 297224
-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