-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_7/scaffold_7_9157137-9374380

-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_18290-T1
Valid prediction for GeneMark_model.30681_t
Valid prediction for GlimmerHMM_glimmerT_18303-T1
Valid prediction for GeneMark_model.30678_t
Valid prediction for Augustus_model.g12316.t1
Valid prediction for Augustus_model.g12315.t1
Valid prediction for GlimmerHMM_glimmerT_18300-T1
Valid prediction for snap_scaffold_7-snap.1835-T1
Valid prediction for HiQ_model.g12322.t1
Valid prediction for GeneMark_model.30698_t
Valid prediction for snap_scaffold_7-snap.1838-T1
Valid prediction for CodingQuarry_transcript_57436-T1
Valid prediction for snap_scaffold_7-snap.1833-T1
Valid prediction for snap_scaffold_7-snap.1815-T1
Valid prediction for Augustus_model.g12319.t1
Valid prediction for snap_scaffold_7-snap.1819-T1
Valid prediction for snap_scaffold_7-snap.1840-T1
Valid prediction for GeneMark_model.30668_t
Valid prediction for GlimmerHMM_glimmerT_18292-T1
Valid prediction for Augustus_model.g12312.t1
Valid prediction for Augustus_model.g12314.t1
Valid prediction for snap_scaffold_7-snap.1811-T1
Valid prediction for GeneMark_model.30682_t
Valid prediction for snap_scaffold_7-snap.1820-T1
Valid prediction for GeneMark_model.30674_t
Valid prediction for HiQ_model.g12324.t1
Valid prediction for snap_scaffold_7-snap.1831-T1
Valid prediction for GeneMark_model.30669_t
Valid prediction for GlimmerHMM_glimmerT_18304-T1
Valid prediction for GeneMark_model.30686_t
Valid prediction for snap_scaffold_7-snap.1829-T1
Valid prediction for snap_scaffold_7-snap.1842-T1
Valid prediction for Augustus_model.g12321.t1
Valid prediction for GeneMark_model.30677_t
Valid prediction for snap_scaffold_7-snap.1818-T1
Valid prediction for snap_scaffold_7-snap.1841-T1
Valid prediction for snap_scaffold_7-snap.1814-T1
Valid prediction for GeneMark_model.30700_t
Couldn't classify 129207, 129221
Sorry, prediction pasa_asmbl_50956.p1 fails validation.
(ATG)	 GG	121427-121627	GT	CTG
(GTG)	 AG	122880-123024	GT	AAG
(GCC)	 AG	123886-124037	GT	CTG
(GTT)	 AG	124542-124622	GT	TGG
(GTG)	 AG	125127-125276	GT	CTG
(GTG)	 AG	125549-125692	GT	AGG
(GTG)	 AG	125911-126009	GT	AGG
(ATC)	 AG	126737-126910	GT	TGG
(GGC)	 AG	127943-128203	GT	CGG
(TGG)	 AG	128517-128633	GT	GGG
(ATC)	 AG	128997-129086	GT	CAG
(GCT)	 AG	129207-129221	GA	AAG
-recovered pasa_asmbl_50956.p1, initial, 121427, 121627
-recovered pasa_asmbl_50956.p1, internal, 122880, 123024
-recovered pasa_asmbl_50956.p1, internal, 123886, 124037
-recovered pasa_asmbl_50956.p1, internal, 124542, 124622
-recovered pasa_asmbl_50956.p1, internal, 125127, 125276
-recovered pasa_asmbl_50956.p1, internal, 125549, 125692
-recovered pasa_asmbl_50956.p1, internal, 125911, 126009
-recovered pasa_asmbl_50956.p1, internal, 126737, 126910
-recovered pasa_asmbl_50956.p1, internal, 127943, 128203
-recovered pasa_asmbl_50956.p1, internal, 128517, 128633
-recovered pasa_asmbl_50956.p1, internal, 128997, 129086
Valid prediction for GeneMark_model.30695_t
Valid prediction for GeneMark_model.30685_t
Valid prediction for GlimmerHMM_glimmerT_18302-T1
Valid prediction for pasa_asmbl_50958.p1
Valid prediction for GeneMark_model.30693_t
Valid prediction for snap_scaffold_7-snap.1816-T1
Valid prediction for GlimmerHMM_glimmerT_18293-T1
Valid prediction for snap_scaffold_7-snap.1837-T1
Valid prediction for GeneMark_model.30683_t
Valid prediction for GeneMark_model.30671_t
Valid prediction for snap_scaffold_7-snap.1817-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.30672_t
Valid prediction for Augustus_model.g12311.t1
Valid prediction for GlimmerHMM_glimmerT_18297-T1
Valid prediction for snap_scaffold_7-snap.1832-T1
Valid prediction for snap_scaffold_7-snap.1828-T1
Valid prediction for snap_scaffold_7-snap.1827-T1
Valid prediction for GeneMark_model.30675_t
Couldn't classify 129255, 129330
Sorry, prediction pasa_asmbl_50957.p1 fails validation.
(CCC)	 AC	129255-129330	GT	TGG
(ATG)	 AG	129564-129659	GT	AGG
(AGA)	 AG	129772-130010	TT	AAT
add_exon() Sorry, pasa_asmbl_50957.p1 129564-129659-initial-1 is invalid.
-recovered pasa_asmbl_50957.p1, initial, 129564, 129659
-recovered pasa_asmbl_50957.p1, terminal, 129772, 130010
-recovered pasa_asmbl_50957.p1, internal, 129564, 129659
Valid prediction for GlimmerHMM_glimmerT_18289-T1
Valid prediction for HiQ_model.g12318.t1
Valid prediction for GeneMark_model.30691_t
Valid prediction for GlimmerHMM_glimmerT_18298-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.30690_t
Valid prediction for GeneMark_model.30684_t
Valid prediction for GeneMark_model.30679_t
Valid prediction for GlimmerHMM_glimmerT_18294-T1
Valid prediction for snap_scaffold_7-snap.1812-T1
Valid prediction for GeneMark_model.30692_t
Valid prediction for GeneMark_model.30694_t
Valid prediction for Augustus_model.g12317.t1
Valid prediction for GeneMark_model.30688_t
Valid prediction for GeneMark_model.30697_t
Valid prediction for GlimmerHMM_glimmerT_18301-T1
Valid prediction for GlimmerHMM_glimmerT_18299-T1
Valid prediction for GeneMark_model.30689_t
Valid prediction for GeneMark_model.30670_t
Valid prediction for GeneMark_model.30676_t
Valid prediction for snap_scaffold_7-snap.1825-T1
Valid prediction for GeneMark_model.30699_t
Valid prediction for snap_scaffold_7-snap.1824-T1
Valid prediction for HiQ_model.g12320.t1
Valid prediction for CodingQuarry_transcript_57435-T1
Valid prediction for snap_scaffold_7-snap.1822-T1
Valid prediction for GlimmerHMM_glimmerT_18306-T1
Valid prediction for snap_scaffold_7-snap.1834-T1
Valid prediction for GlimmerHMM_glimmerT_18296-T1
Valid prediction for snap_scaffold_7-snap.1823-T1
Valid prediction for CodingQuarry_transcript_57437-T1
Valid prediction for Augustus_model.g12325.t1
Valid prediction for pasa_asmbl_49856.p1
Valid prediction for GlimmerHMM_glimmerT_18291-T1
Valid prediction for pasa_asmbl_49858.p1
Valid prediction for GlimmerHMM_glimmerT_18295-T1
Valid prediction for snap_scaffold_7-snap.1813-T1
Valid prediction for snap_scaffold_7-snap.1821-T1
Valid prediction for snap_scaffold_7-snap.1836-T1
Valid prediction for GeneMark_model.30680_t
Valid prediction for GlimmerHMM_glimmerT_18305-T1
Valid prediction for Augustus_model.g12323.t1
Valid prediction for snap_scaffold_7-snap.1830-T1
Valid prediction for snap_scaffold_7-snap.1839-T1
Valid prediction for GeneMark_model.30687_t
Valid prediction for GeneMark_model.30673_t
Valid prediction for Augustus_model.g12313.t1
Valid prediction for snap_scaffold_7-snap.1826-T1
Valid prediction for GeneMark_model.30696_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 192933, rend_intergenic: 189174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199856, rend_intergenic: 194077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 217244
-exon list size: 393


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.5    
1.8    
2.0    
2.3    
2.5    
2.8    
3.0    
3.3    
3.5    
3.8    
4.1    
4.3    
4.6    
4.8    
5.1    
5.3    
5.6    
5.8    
6.1    
6.3    
6.6    
6.8    
7.1    
7.3    
7.6    
7.8    
8.1    
8.4    
8.6    
8.9    
9.1    
9.4    
9.6    
9.9    
10.1    
10.4    
10.6    
10.9    
11.1    
11.4    
11.6    
11.9    
12.2    
12.4    
12.7    
12.9    
13.2    
13.4    
13.7    
13.9    
14.2    
14.4    
14.7    
14.9    
15.2    
15.4    
15.7    
15.9    
16.2    
16.5    
16.7    
17.0    
17.2    
17.5    
17.7    
18.0    
18.2    
18.5    
18.7    
19.0    
19.2    
19.5    
19.7    
20.0    
20.3    
20.5    
20.8    
21.0    
21.3    
21.5    
21.8    
22.0    
22.3    
22.5    
22.8    
23.0    
23.3    
23.5    
23.8    
24.1    
24.3    
24.6    
24.8    
25.1    
25.3    
25.6    
25.8    
26.1    
26.3    
26.6    
26.8    
27.1    
27.3    
27.6    
27.8    
28.1    
28.4    
28.6    
28.9    
29.1    
29.4    
29.6    
29.9    
30.1    
30.4    
30.6    
30.9    
31.1    
31.4    
31.6    
31.9    
32.2    
32.4    
32.7    
32.9    
33.2    
33.4    
33.7    
33.9    
34.2    
34.4    
34.7    
34.9    
35.2    
35.4    
35.7    
35.9    
36.2    
36.5    
36.7    
37.0    
37.2    
37.5    
37.7    
38.0    
38.2    
38.5    
38.7    
39.0    
39.2    
39.5    
39.7    
40.0    
40.3    
40.5    
40.8    
41.0    
41.3    
41.5    
41.8    
42.0    
42.3    
42.5    
42.8    
43.0    
43.3    
43.5    
43.8    
44.1    
44.3    
44.6    
44.8    
45.1    
45.3    
45.6    
45.8    
46.1    
46.3    
46.6    
46.8    
47.1    
47.3    
47.6    
47.8    
48.1    
48.4    
48.6    
48.9    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.1    
51.4    
51.6    
51.9    
52.2    
52.4    
52.7    
52.9    
53.2    
53.4    
53.7    
53.9    
54.2    
54.4    
54.7    
54.9    
55.2    
55.4    
55.7    
55.9    
56.2    
56.5    
56.7    
57.0    
57.2    
57.5    
57.7    
58.0    
58.2    
58.5    
58.7    
59.0    
59.2    
59.5    
59.7    
60.0    
60.3    
60.5    
60.8    
61.0    
61.3    
61.5    
61.8    
62.0    
62.3    
62.5    
62.8    
63.0    
63.3    
63.5    
63.8    
64.1    
64.3    
64.6    
64.8    
65.1    
65.3    
65.6    
65.8    
66.1    
66.3    
66.6    
66.8    
67.1    
67.3    
67.6    
67.8    
68.1    
68.4    
68.6    
68.9    
69.1    
69.4    
69.6    
69.9    
70.1    
70.4    
70.6    
70.9    
71.1    
71.4    
71.6    
71.9    
72.2    
72.4    
72.7    
72.9    
73.2    
73.4    
73.7    
73.9    
74.2    
74.4    
74.7    
74.9    
75.2    
75.4    
75.7    
75.9    
76.2    
76.5    
76.7    
77.0    
77.2    
77.5    
77.7    
78.0    
78.2    
78.5    
78.7    
79.0    
79.2    
79.5    
79.7    
80.0    
80.3    
80.5    
80.8    
81.0    
81.3    
81.5    
81.8    
82.0    
82.3    
82.5    
82.8    
83.0    
83.3    
83.5    
83.8    
84.1    
84.3    
84.6    
84.8    
85.1    
85.3    
85.6    
85.8    
86.1    
86.3    
86.6    
86.8    
87.1    
87.3    
87.6    
87.8    
88.1    
88.4    
88.6    
88.9    
89.1    
89.4    
89.6    
89.9    
90.1    
90.4    
90.6    
90.9    
91.1    
91.4    
91.6    
91.9    
92.2    
92.4    
92.7    
92.9    
93.2    
93.4    
93.7    
93.9    
94.2    
94.4    
94.7    
94.9    
95.2    
95.4    
95.7    
95.9    
96.2    
96.5    
96.7    
97.0    
97.2    
97.5    
97.7    
98.0    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 192933, rend_intergenic: 189174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199856, rend_intergenic: 194077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 199126 - 217244
-exon list size: 31


building trellis

3.0    
6.1    
9.1    
12.1    
15.2    
18.2    
21.2    
24.2    
27.3    
30.3    
33.3    
36.4    
39.4    
42.4    
45.5    
48.5    
51.5    
54.5    
57.6    
60.6    
63.6    
66.7    
69.7    
72.7    
75.8    
78.8    
81.8    
84.8    
87.9    
90.9    
93.9    
97.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 199126 - 213006
-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