-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_9/scaffold_9_9006479-9250413

-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_9-snap.1859-T1
Valid prediction for GeneMark_model.39621_t
Valid prediction for GeneMark_model.39616_t
Valid prediction for GeneMark_model.39604_t
Valid prediction for GlimmerHMM_glimmerT_23129-T1
Valid prediction for GeneMark_model.39610_t
Valid prediction for GlimmerHMM_glimmerT_23136-T1
Valid prediction for GlimmerHMM_glimmerT_23121-T1
Valid prediction for snap_scaffold_9-snap.1849-T1
Valid prediction for GlimmerHMM_glimmerT_23125-T1
Valid prediction for GeneMark_model.39612_t
Valid prediction for GeneMark_model.39637_t
Valid prediction for GlimmerHMM_glimmerT_23135-T1
Valid prediction for GeneMark_model.39627_t
Valid prediction for GeneMark_model.39625_t
Valid prediction for GeneMark_model.39602_t
Valid prediction for GeneMark_model.39629_t
Valid prediction for GlimmerHMM_glimmerT_23127-T1
Valid prediction for GeneMark_model.39636_t
Valid prediction for snap_scaffold_9-snap.1845-T1
Valid prediction for snap_scaffold_9-snap.1839-T1
Valid prediction for GeneMark_model.39605_t
Valid prediction for snap_scaffold_9-snap.1832-T1
Valid prediction for GeneMark_model.39611_t
Valid prediction for GeneMark_model.39606_t
Valid prediction for GeneMark_model.39632_t
Valid prediction for snap_scaffold_9-snap.1835-T1
Valid prediction for snap_scaffold_9-snap.1838-T1
Valid prediction for Augustus_model.g15491.t1
Valid prediction for snap_scaffold_9-snap.1847-T1
Valid prediction for snap_scaffold_9-snap.1840-T1
Valid prediction for GeneMark_model.39623_t
Valid prediction for snap_scaffold_9-snap.1843-T1
Valid prediction for Augustus_model.g15498.t1
Valid prediction for GeneMark_model.39622_t
Valid prediction for snap_scaffold_9-snap.1842-T1
Valid prediction for Augustus_model.g15489.t1
Valid prediction for Augustus_model.g15494.t1
Valid prediction for snap_scaffold_9-snap.1846-T1
Valid prediction for GeneMark_model.39613_t
Valid prediction for GlimmerHMM_glimmerT_23124-T1
Valid prediction for GeneMark_model.39615_t
Valid prediction for snap_scaffold_9-snap.1837-T1
Valid prediction for snap_scaffold_9-snap.1856-T1
Valid prediction for snap_scaffold_9-snap.1853-T1
Valid prediction for Augustus_model.g15497.t1
Valid prediction for GeneMark_model.39614_t
Valid prediction for GeneMark_model.39624_t
Valid prediction for GlimmerHMM_glimmerT_23131-T1
Valid prediction for GlimmerHMM_glimmerT_23130-T1
Valid prediction for GeneMark_model.39628_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 Augustus_model.g15493.t1
Valid prediction for GeneMark_model.39603_t
Valid prediction for snap_scaffold_9-snap.1850-T1
Valid prediction for Augustus_model.g15490.t1
Valid prediction for GlimmerHMM_glimmerT_23133-T1
Valid prediction for GlimmerHMM_glimmerT_23123-T1
Valid prediction for snap_scaffold_9-snap.1844-T1
Valid prediction for CodingQuarry_transcript_62095-T1
Valid prediction for snap_scaffold_9-snap.1841-T1
Valid prediction for snap_scaffold_9-snap.1833-T1
Valid prediction for GlimmerHMM_glimmerT_23132-T1
Valid prediction for GeneMark_model.39618_t
Valid prediction for GlimmerHMM_glimmerT_23134-T1
Valid prediction for snap_scaffold_9-snap.1855-T1
Valid prediction for snap_scaffold_9-snap.1854-T1
Valid prediction for snap_scaffold_9-snap.1852-T1
Valid prediction for snap_scaffold_9-snap.1851-T1
Valid prediction for GeneMark_model.39633_t
Valid prediction for GlimmerHMM_glimmerT_23128-T1
Valid prediction for GeneMark_model.39609_t
Valid prediction for snap_scaffold_9-snap.1836-T1
Valid prediction for Augustus_model.g15492.t1
Valid prediction for GeneMark_model.39619_t
Valid prediction for GeneMark_model.39631_t
Valid prediction for snap_scaffold_9-snap.1857-T1
Valid prediction for GeneMark_model.39620_t
Valid prediction for GeneMark_model.39635_t
Valid prediction for GeneMark_model.39630_t
Valid prediction for snap_scaffold_9-snap.1834-T1
Valid prediction for snap_scaffold_9-snap.1860-T1
Valid prediction for GeneMark_model.39617_t
Valid prediction for Augustus_model.g15496.t1
Valid prediction for GlimmerHMM_glimmerT_23126-T1
Valid prediction for Augustus_model.g15495.t1
Valid prediction for GlimmerHMM_glimmerT_23122-T1
Valid prediction for GeneMark_model.39634_t
Valid prediction for snap_scaffold_9-snap.1848-T1
Valid prediction for snap_scaffold_9-snap.1858-T1
Valid prediction for snap_scaffold_9-snap.1861-T1
Valid prediction for GeneMark_model.39608_t
Valid prediction for GeneMark_model.39626_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 203411, rend_intergenic: 200889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207942, rend_intergenic: 205020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 243935
-exon list size: 329


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.4    
2.7    
3.0    
3.3    
3.6    
3.9    
4.2    
4.5    
4.8    
5.1    
5.4    
5.7    
6.0    
6.3    
6.6    
6.9    
7.3    
7.6    
7.9    
8.2    
8.5    
8.8    
9.1    
9.4    
9.7    
10.0    
10.3    
10.6    
10.9    
11.2    
11.5    
11.8    
12.1    
12.4    
12.7    
13.0    
13.3    
13.6    
13.9    
14.2    
14.5    
14.8    
15.1    
15.4    
15.7    
16.0    
16.3    
16.6    
16.9    
17.2    
17.5    
17.8    
18.1    
18.4    
18.7    
19.0    
19.3    
19.6    
19.9    
20.2    
20.5    
20.8    
21.1    
21.5    
21.8    
22.1    
22.4    
22.7    
23.0    
23.3    
23.6    
23.9    
24.2    
24.5    
24.8    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
26.9    
27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
29.0    
29.3    
29.6    
29.9    
30.2    
30.5    
30.8    
31.1    
31.4    
31.7    
32.0    
32.3    
32.6    
32.9    
33.2    
33.5    
33.8    
34.1    
34.4    
34.7    
35.0    
35.3    
35.6    
36.0    
36.3    
36.6    
36.9    
37.2    
37.5    
37.8    
38.1    
38.4    
38.7    
39.0    
39.3    
39.6    
39.9    
40.2    
40.5    
40.8    
41.1    
41.4    
41.7    
42.0    
42.3    
42.6    
42.9    
43.2    
43.5    
43.8    
44.1    
44.4    
44.7    
45.0    
45.3    
45.6    
45.9    
46.2    
46.5    
46.8    
47.1    
47.4    
47.7    
48.0    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
52.0    
52.3    
52.6    
52.9    
53.2    
53.5    
53.8    
54.1    
54.4    
54.7    
55.0    
55.3    
55.6    
55.9    
56.2    
56.5    
56.8    
57.1    
57.4    
57.7    
58.0    
58.3    
58.6    
58.9    
59.2    
59.5    
59.8    
60.1    
60.4    
60.7    
61.0    
61.3    
61.6    
61.9    
62.2    
62.5    
62.8    
63.1    
63.4    
63.7    
64.0    
64.4    
64.7    
65.0    
65.3    
65.6    
65.9    
66.2    
66.5    
66.8    
67.1    
67.4    
67.7    
68.0    
68.3    
68.6    
68.9    
69.2    
69.5    
69.8    
70.1    
70.4    
70.7    
71.0    
71.3    
71.6    
71.9    
72.2    
72.5    
72.8    
73.1    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.2    
75.5    
75.8    
76.1    
76.4    
76.7    
77.0    
77.3    
77.6    
77.9    
78.2    
78.5    
78.9    
79.2    
79.5    
79.8    
80.1    
80.4    
80.7    
81.0    
81.3    
81.6    
81.9    
82.2    
82.5    
82.8    
83.1    
83.4    
83.7    
84.0    
84.3    
84.6    
84.9    
85.2    
85.5    
85.8    
86.1    
86.4    
86.7    
87.0    
87.3    
87.6    
87.9    
88.2    
88.5    
88.8    
89.1    
89.4    
89.7    
90.0    
90.3    
90.6    
90.9    
91.2    
91.5    
91.8    
92.1    
92.4    
92.7    
93.1    
93.4    
93.7    
94.0    
94.3    
94.6    
94.9    
95.2    
95.5    
95.8    
96.1    
96.4    
96.7    
97.0    
97.3    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 19 predictions from path traversal
Error with prediction: snap lend_intergenic: 203411, rend_intergenic: 200889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207942, rend_intergenic: 205020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 11 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 207736 - 243935
-exon list size: 32


building trellis

2.9    
5.9    
8.8    
11.8    
14.7    
17.6    
20.6    
23.5    
26.5    
29.4    
32.4    
35.3    
38.2    
41.2    
44.1    
47.1    
50.0    
52.9    
55.9    
58.8    
61.8    
64.7    
67.6    
70.6    
73.5    
76.5    
79.4    
82.4    
85.3    
88.2    
91.2    
94.1    
97.1    
-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 209772 - 243935
-exon list size: 25


building trellis

3.7    
7.4    
11.1    
14.8    
18.5    
22.2    
25.9    
29.6    
33.3    
37.0    
40.7    
44.4    
48.1    
51.9    
55.6    
59.3    
63.0    
66.7    
70.4    
74.1    
77.8    
81.5    
85.2    
88.9    
92.6    
96.3    
-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 217938 - 243935
-exon list size: 21


building trellis

4.3    
8.7    
13.0    
17.4    
21.7    
26.1    
30.4    
34.8    
39.1    
43.5    
47.8    
52.2    
56.5    
60.9    
65.2    
69.6    
73.9    
78.3    
82.6    
87.0    
91.3    
95.7    
-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 217938 - 242390
-exon list size: 20


building trellis

4.5    
9.1    
13.6    
18.2    
22.7    
27.3    
31.8    
36.4    
40.9    
45.5    
50.0    
54.5    
59.1    
63.6    
68.2    
72.7    
77.3    
81.8    
86.4    
90.9    
95.5    
-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 217938 - 228257
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-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 228266 - 242390
-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
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 228417 - 242390
-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 228475 - 242390
-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 228475 - 239459
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-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