-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_9/scaffold_9_9248877-9430518

-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 CodingQuarry_transcript_62097-T1
Valid prediction for snap_scaffold_9-snap.1875-T1
Valid prediction for snap_scaffold_9-snap.1889-T1
Valid prediction for GeneMark_model.39669_t
Valid prediction for GeneMark_model.39665_t
Valid prediction for GeneMark_model.39660_t
Valid prediction for GeneMark_model.39644_t
Valid prediction for GeneMark_model.39658_t
Valid prediction for GeneMark_model.39651_t
Valid prediction for GeneMark_model.39664_t
Valid prediction for GlimmerHMM_glimmerT_23152-T1
Valid prediction for GlimmerHMM_glimmerT_23141-T1
Valid prediction for GeneMark_model.39662_t
Valid prediction for GeneMark_model.39666_t
Valid prediction for GlimmerHMM_glimmerT_23140-T1
Valid prediction for GeneMark_model.39654_t
Valid prediction for GeneMark_model.39673_t
Valid prediction for GlimmerHMM_glimmerT_23149-T1
Valid prediction for GeneMark_model.39657_t
Valid prediction for GeneMark_model.39652_t
Valid prediction for GlimmerHMM_glimmerT_23138-T1
Valid prediction for snap_scaffold_9-snap.1876-T1
Valid prediction for GlimmerHMM_glimmerT_23147-T1
Valid prediction for snap_scaffold_9-snap.1884-T1
Valid prediction for GeneMark_model.39640_t
Valid prediction for GlimmerHMM_glimmerT_23150-T1
Valid prediction for GeneMark_model.39646_t
Valid prediction for snap_scaffold_9-snap.1869-T1
Valid prediction for snap_scaffold_9-snap.1882-T1
Valid prediction for GeneMark_model.39671_t
Valid prediction for snap_scaffold_9-snap.1867-T1
Valid prediction for GlimmerHMM_glimmerT_23158-T1
Couldn't classify 119572, 119760
Sorry, prediction pasa_asmbl_54186.p1 fails validation.
(TCA)	 AC	119572-119760	GT	GGG
(ATG)	 AG	120212-121076	GT	TGG
(ACA)	 AG	121177-121295	AA	AGA
-recovered pasa_asmbl_54186.p1, initial, 120212, 121076
-recovered pasa_asmbl_54186.p1, terminal, 121177, 121295
-recovered pasa_asmbl_54186.p1, internal, 120212, 121076
Valid prediction for snap_scaffold_9-snap.1894-T1
Valid prediction for snap_scaffold_9-snap.1871-T1
Valid prediction for GeneMark_model.39675_t
Valid prediction for snap_scaffold_9-snap.1868-T1
Valid prediction for snap_scaffold_9-snap.1885-T1
Valid prediction for GlimmerHMM_glimmerT_23155-T1
Valid prediction for snap_scaffold_9-snap.1890-T1
Valid prediction for snap_scaffold_9-snap.1892-T1
Couldn't classify 156207, 156366
Couldn't classify 156967, 157016
Sorry, prediction pasa_asmbl_54698.p1 fails validation.
(AGG)	 CT	156207-156366	GT	AGG
(AGA)	 AG	156508-156693	GT	CAG
(CGT)	 AG	156967-157016	GG	AGG
-recovered pasa_asmbl_54698.p1, internal, 156508, 156693
Valid prediction for snap_scaffold_9-snap.1862-T1
Valid prediction for HiQ_model.g15507.t1
Valid prediction for GeneMark_model.39648_t
Valid prediction for GeneMark_model.39678_t
Valid prediction for GlimmerHMM_glimmerT_23151-T1
Valid prediction for GlimmerHMM_glimmerT_23160-T1
Valid prediction for Augustus_model.g15509.t1
Valid prediction for GlimmerHMM_glimmerT_23148-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.39643_t
Valid prediction for Augustus_model.g15502.t1
Valid prediction for GeneMark_model.39642_t
Valid prediction for Augustus_model.g15504.t1
Valid prediction for GlimmerHMM_glimmerT_23142-T1
Valid prediction for GlimmerHMM_glimmerT_23159-T1
Valid prediction for Augustus_model.g15506.t1
Valid prediction for snap_scaffold_9-snap.1887-T1
Valid prediction for GlimmerHMM_glimmerT_23145-T1
Valid prediction for snap_scaffold_9-snap.1877-T1
Valid prediction for GeneMark_model.39650_t
Valid prediction for GeneMark_model.39674_t
Valid prediction for GlimmerHMM_glimmerT_23161-T1
Valid prediction for snap_scaffold_9-snap.1878-T1
Valid prediction for GeneMark_model.39655_t
Valid prediction for GeneMark_model.39649_t
Valid prediction for GeneMark_model.39647_t
Valid prediction for snap_scaffold_9-snap.1863-T1
Valid prediction for GlimmerHMM_glimmerT_23157-T1
Valid prediction for GeneMark_model.39661_t
Valid prediction for GeneMark_model.39679_t
Valid prediction for snap_scaffold_9-snap.1865-T1
Valid prediction for Augustus_model.g15510.t1
Valid prediction for GeneMark_model.39672_t
Valid prediction for snap_scaffold_9-snap.1866-T1
Valid prediction for pasa_asmbl_55126.p1
Valid prediction for Augustus_model.g15499.t1
Valid prediction for GeneMark_model.39639_t
Valid prediction for GlimmerHMM_glimmerT_23146-T1
Valid prediction for GeneMark_model.39645_t
Valid prediction for Augustus_model.g15503.t1
Valid prediction for GeneMark_model.39677_t
Valid prediction for pasa_asmbl_55132.p1
Valid prediction for Augustus_model.g15500.t1
Valid prediction for GeneMark_model.39676_t
Valid prediction for CodingQuarry_transcript_62096-T1
Valid prediction for GeneMark_model.39670_t
Valid prediction for GlimmerHMM_glimmerT_23144-T1
Valid prediction for GeneMark_model.39667_t
Valid prediction for GeneMark_model.39659_t
Valid prediction for GlimmerHMM_glimmerT_23139-T1
Valid prediction for GlimmerHMM_glimmerT_23153-T1
Valid prediction for snap_scaffold_9-snap.1879-T1
Valid prediction for Augustus_model.g15511.t1
Valid prediction for snap_scaffold_9-snap.1883-T1
Valid prediction for GeneMark_model.39656_t
Valid prediction for GeneMark_model.39668_t
Valid prediction for GeneMark_model.39680_t
Valid prediction for GlimmerHMM_glimmerT_23156-T1
Valid prediction for snap_scaffold_9-snap.1873-T1
Valid prediction for Augustus_model.g15508.t1
Valid prediction for snap_scaffold_9-snap.1870-T1
Valid prediction for snap_scaffold_9-snap.1888-T1
Valid prediction for GlimmerHMM_glimmerT_23143-T1
Valid prediction for snap_scaffold_9-snap.1872-T1
Valid prediction for snap_scaffold_9-snap.1874-T1
Valid prediction for HiQ_model.g15505.t1
Valid prediction for GeneMark_model.39653_t
Valid prediction for snap_scaffold_9-snap.1893-T1
Valid prediction for snap_scaffold_9-snap.1881-T1
Valid prediction for GlimmerHMM_glimmerT_23154-T1
Valid prediction for Augustus_model.g15501.t1
Valid prediction for snap_scaffold_9-snap.1864-T1
Valid prediction for GeneMark_model.39663_t
Valid prediction for snap_scaffold_9-snap.1886-T1
Valid prediction for snap_scaffold_9-snap.1891-T1
Valid prediction for snap_scaffold_9-snap.1880-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 51062, rend_intergenic: 37748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58532, rend_intergenic: 54315  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80808, rend_intergenic: 74211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139846, rend_intergenic: 122510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152581, rend_intergenic: 146724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163176, rend_intergenic: 158268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166159, rend_intergenic: 165102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168632, rend_intergenic: 166184  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174378, rend_intergenic: 168647  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 181642
-exon list size: 571


building trellis

0.2    
0.3    
0.5    
0.7    
0.9    
1.0    
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1.4    
1.6    
1.7    
1.9    
2.1    
2.3    
2.4    
2.6    
2.8    
3.0    
3.1    
3.3    
3.5    
3.7    
3.8    
4.0    
4.2    
4.4    
4.5    
4.7    
4.9    
5.1    
5.2    
5.4    
5.6    
5.8    
5.9    
6.1    
6.3    
6.5    
6.6    
6.8    
7.0    
7.2    
7.3    
7.5    
7.7    
7.9    
8.0    
8.2    
8.4    
8.6    
8.7    
8.9    
9.1    
9.2    
9.4    
9.6    
9.8    
9.9    
10.1    
10.3    
10.5    
10.6    
10.8    
11.0    
11.2    
11.3    
11.5    
11.7    
11.9    
12.0    
12.2    
12.4    
12.6    
12.7    
12.9    
13.1    
13.3    
13.4    
13.6    
13.8    
14.0    
14.1    
14.3    
14.5    
14.7    
14.8    
15.0    
15.2    
15.4    
15.5    
15.7    
15.9    
16.1    
16.2    
16.4    
16.6    
16.8    
16.9    
17.1    
17.3    
17.5    
17.6    
17.8    
18.0    
18.2    
18.3    
18.5    
18.7    
18.8    
19.0    
19.2    
19.4    
19.5    
19.7    
19.9    
20.1    
20.2    
20.4    
20.6    
20.8    
20.9    
21.1    
21.3    
21.5    
21.6    
21.8    
22.0    
22.2    
22.3    
22.5    
22.7    
22.9    
23.0    
23.2    
23.4    
23.6    
23.7    
23.9    
24.1    
24.3    
24.4    
24.6    
24.8    
25.0    
25.1    
25.3    
25.5    
25.7    
25.8    
26.0    
26.2    
26.4    
26.5    
26.7    
26.9    
27.1    
27.2    
27.4    
27.6    
27.7    
27.9    
28.1    
28.3    
28.4    
28.6    
28.8    
29.0    
29.1    
29.3    
29.5    
29.7    
29.8    
30.0    
30.2    
30.4    
30.5    
30.7    
30.9    
31.1    
31.2    
31.4    
31.6    
31.8    
31.9    
32.1    
32.3    
32.5    
32.6    
32.8    
33.0    
33.2    
33.3    
33.5    
33.7    
33.9    
34.0    
34.2    
34.4    
34.6    
34.7    
34.9    
35.1    
35.3    
35.4    
35.6    
35.8    
36.0    
36.1    
36.3    
36.5    
36.6    
36.8    
37.0    
37.2    
37.3    
37.5    
37.7    
37.9    
38.0    
38.2    
38.4    
38.6    
38.7    
38.9    
39.1    
39.3    
39.4    
39.6    
39.8    
40.0    
40.1    
40.3    
40.5    
40.7    
40.8    
41.0    
41.2    
41.4    
41.5    
41.7    
41.9    
42.1    
42.2    
42.4    
42.6    
42.8    
42.9    
43.1    
43.3    
43.5    
43.6    
43.8    
44.0    
44.2    
44.3    
44.5    
44.7    
44.9    
45.0    
45.2    
45.4    
45.5    
45.7    
45.9    
46.1    
46.2    
46.4    
46.6    
46.8    
46.9    
47.1    
47.3    
47.5    
47.6    
47.8    
48.0    
48.2    
48.3    
48.5    
48.7    
48.9    
49.0    
49.2    
49.4    
49.6    
49.7    
49.9    
50.1    
50.3    
50.4    
50.6    
50.8    
51.0    
51.1    
51.3    
51.5    
51.7    
51.8    
52.0    
52.2    
52.4    
52.5    
52.7    
52.9    
53.1    
53.2    
53.4    
53.6    
53.8    
53.9    
54.1    
54.3    
54.5    
54.6    
54.8    
55.0    
55.1    
55.3    
55.5    
55.7    
55.8    
56.0    
56.2    
56.4    
56.5    
56.7    
56.9    
57.1    
57.2    
57.4    
57.6    
57.8    
57.9    
58.1    
58.3    
58.5    
58.6    
58.8    
59.0    
59.2    
59.3    
59.5    
59.7    
59.9    
60.0    
60.2    
60.4    
60.6    
60.7    
60.9    
61.1    
61.3    
61.4    
61.6    
61.8    
62.0    
62.1    
62.3    
62.5    
62.7    
62.8    
63.0    
63.2    
63.4    
63.5    
63.7    
63.9    
64.0    
64.2    
64.4    
64.6    
64.7    
64.9    
65.1    
65.3    
65.4    
65.6    
65.8    
66.0    
66.1    
66.3    
66.5    
66.7    
66.8    
67.0    
67.2    
67.4    
67.5    
67.7    
67.9    
68.1    
68.2    
68.4    
68.6    
68.8    
68.9    
69.1    
69.3    
69.5    
69.6    
69.8    
70.0    
70.2    
70.3    
70.5    
70.7    
70.9    
71.0    
71.2    
71.4    
71.6    
71.7    
71.9    
72.1    
72.3    
72.4    
72.6    
72.8    
72.9    
73.1    
73.3    
73.5    
73.6    
73.8    
74.0    
74.2    
74.3    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.6    
75.7    
75.9    
76.1    
76.3    
76.4    
76.6    
76.8    
77.0    
77.1    
77.3    
77.5    
77.7    
77.8    
78.0    
78.2    
78.4    
78.5    
78.7    
78.9    
79.1    
79.2    
79.4    
79.6    
79.8    
79.9    
80.1    
80.3    
80.5    
80.6    
80.8    
81.0    
81.2    
81.3    
81.5    
81.7    
81.8    
82.0    
82.2    
82.4    
82.5    
82.7    
82.9    
83.1    
83.2    
83.4    
83.6    
83.8    
83.9    
84.1    
84.3    
84.5    
84.6    
84.8    
85.0    
85.2    
85.3    
85.5    
85.7    
85.9    
86.0    
86.2    
86.4    
86.6    
86.7    
86.9    
87.1    
87.3    
87.4    
87.6    
87.8    
88.0    
88.1    
88.3    
88.5    
88.7    
88.8    
89.0    
89.2    
89.4    
89.5    
89.7    
89.9    
90.1    
90.2    
90.4    
90.6    
90.8    
90.9    
91.1    
91.3    
91.4    
91.6    
91.8    
92.0    
92.1    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.4    
93.5    
93.7    
93.9    
94.1    
94.2    
94.4    
94.6    
94.8    
94.9    
95.1    
95.3    
95.5    
95.6    
95.8    
96.0    
96.2    
96.3    
96.5    
96.7    
96.9    
97.0    
97.2    
97.4    
97.6    
97.7    
97.9    
98.1    
98.3    
98.4    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 20 predictions from path traversal
Error with prediction: snap lend_intergenic: 51062, rend_intergenic: 37748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58532, rend_intergenic: 54315  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80808, rend_intergenic: 74211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139846, rend_intergenic: 122510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152581, rend_intergenic: 146724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163176, rend_intergenic: 158268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166159, rend_intergenic: 165102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168632, rend_intergenic: 166184  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174378, rend_intergenic: 168647  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 24020
-exon list size: 26


building trellis

3.6    
7.1    
10.7    
14.3    
17.9    
21.4    
25.0    
28.6    
32.1    
35.7    
39.3    
42.9    
46.4    
50.0    
53.6    
57.1    
60.7    
64.3    
67.9    
71.4    
75.0    
78.6    
82.1    
85.7    
89.3    
92.9    
96.4    
-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 8077 - 24020
-exon list size: 14


building trellis

6.2    
12.5    
18.8    
25.0    
31.2    
37.5    
43.8    
50.0    
56.2    
62.5    
68.8    
75.0    
81.2    
87.5    
93.8    
-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 8077 - 23899
-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

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support