-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_9/scaffold_9_8603730-8851464

-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 GeneMark_model.39547_t
Valid prediction for GlimmerHMM_glimmerT_23093-T1
Valid prediction for snap_scaffold_9-snap.1792-T1
Valid prediction for snap_scaffold_9-snap.1780-T1
Valid prediction for snap_scaffold_9-snap.1771-T1
Valid prediction for GeneMark_model.39544_t
Valid prediction for GeneMark_model.39551_t
Valid prediction for Augustus_model.g15458.t1
Valid prediction for snap_scaffold_9-snap.1778-T1
Valid prediction for GlimmerHMM_glimmerT_23095-T1
Valid prediction for Augustus_model.g15462.t1
Valid prediction for GeneMark_model.39545_t
Valid prediction for GeneMark_model.39548_t
Valid prediction for GlimmerHMM_glimmerT_23079-T1
Valid prediction for GeneMark_model.39549_t
Valid prediction for GeneMark_model.39563_t
Valid prediction for GlimmerHMM_glimmerT_23086-T1
Valid prediction for snap_scaffold_9-snap.1777-T1
Valid prediction for GeneMark_model.39558_t
Valid prediction for GeneMark_model.39561_t
Valid prediction for snap_scaffold_9-snap.1784-T1
Valid prediction for snap_scaffold_9-snap.1776-T1
Valid prediction for Augustus_model.g15466.t1
Valid prediction for GlimmerHMM_glimmerT_23087-T1
Valid prediction for snap_scaffold_9-snap.1772-T1
Valid prediction for snap_scaffold_9-snap.1783-T1
Valid prediction for GlimmerHMM_glimmerT_23081-T1
Valid prediction for snap_scaffold_9-snap.1798-T1
Valid prediction for GlimmerHMM_glimmerT_23085-T1
Valid prediction for snap_scaffold_9-snap.1770-T1
Valid prediction for Augustus_model.g15461.t1
Valid prediction for snap_scaffold_9-snap.1788-T1
Valid prediction for GeneMark_model.39564_t
Valid prediction for snap_scaffold_9-snap.1787-T1
Valid prediction for GlimmerHMM_glimmerT_23091-T1
Valid prediction for Augustus_model.g15460.t1
Valid prediction for snap_scaffold_9-snap.1794-T1
Valid prediction for GlimmerHMM_glimmerT_23076-T1
Valid prediction for GlimmerHMM_glimmerT_23083-T1
Valid prediction for GeneMark_model.39543_t
Valid prediction for GlimmerHMM_glimmerT_23084-T1
Valid prediction for GlimmerHMM_glimmerT_23096-T1
Valid prediction for Augustus_model.g15463.t1
Valid prediction for Augustus_model.g15469.t1
Valid prediction for snap_scaffold_9-snap.1779-T1
Valid prediction for GeneMark_model.39554_t
Valid prediction for GlimmerHMM_glimmerT_23088-T1
Valid prediction for snap_scaffold_9-snap.1782-T1
Valid prediction for GlimmerHMM_glimmerT_23080-T1
Valid prediction for snap_scaffold_9-snap.1773-T1
Valid prediction for snap_scaffold_9-snap.1786-T1
Valid prediction for snap_scaffold_9-snap.1785-T1
Valid prediction for Augustus_model.g15459.t1
Valid prediction for snap_scaffold_9-snap.1796-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.39552_t
Valid prediction for snap_scaffold_9-snap.1789-T1
Valid prediction for GeneMark_model.39556_t
Couldn't classify 20292, 20603
Sorry, prediction pasa_asmbl_55110.p1 fails validation.
(ATG)	 AA	20292-20603	AG	GTA
Valid prediction for GlimmerHMM_glimmerT_23094-T1
Valid prediction for GeneMark_model.39537_t
Valid prediction for Augustus_model.g15467.t1
Valid prediction for CodingQuarry_transcript_62090-T1
Valid prediction for GeneMark_model.39539_t
Valid prediction for GeneMark_model.39555_t
Valid prediction for snap_scaffold_9-snap.1790-T1
Valid prediction for GeneMark_model.39542_t
Valid prediction for snap_scaffold_9-snap.1795-T1
Valid prediction for GeneMark_model.39553_t
Valid prediction for pasa_asmbl_55106.p1
Valid prediction for GeneMark_model.39550_t
Valid prediction for HiQ_model.g15465.t1
Valid prediction for GlimmerHMM_glimmerT_23089-T1
Valid prediction for GeneMark_model.39546_t
Valid prediction for GeneMark_model.39540_t
Valid prediction for snap_scaffold_9-snap.1793-T1
Valid prediction for Augustus_model.g15468.t1
Valid prediction for GlimmerHMM_glimmerT_23077-T1
Valid prediction for snap_scaffold_9-snap.1781-T1
Valid prediction for Augustus_model.g15464.t1
Valid prediction for snap_scaffold_9-snap.1797-T1
Valid prediction for snap_scaffold_9-snap.1774-T1
Couldn't classify 25605, 26250
Sorry, prediction pasa_asmbl_55107.p1 fails validation.
(TCA)	 CT	25605-26250	GT	AGG
(GCC)	 AG	26408-26662	GT	CGG
(GTA)	 AG	26780-27981	TT	GAT
-recovered pasa_asmbl_55107.p1, terminal, 26780, 27981
-recovered pasa_asmbl_55107.p1, internal, 26408, 26662
Couldn't classify 25068, 25523
Sorry, prediction pasa_asmbl_55108.p1 fails validation.
(ATG)	 AC	25068-25523	CA	AGC
Valid prediction for snap_scaffold_9-snap.1775-T1
Valid prediction for GeneMark_model.39562_t
Valid prediction for CodingQuarry_transcript_62091-T1
Valid prediction for GeneMark_model.39541_t
Valid prediction for Augustus_model.g15457.t1
Couldn't classify 44729, 44908
Sorry, prediction pasa_asmbl_55785.p1 fails validation.
(GAC)	 CA	44729-44908	GT	AGG
(GAG)	 AG	45069-45194	TG	AAT
-recovered pasa_asmbl_55785.p1, terminal, 45069, 45194
Valid prediction for GlimmerHMM_glimmerT_23090-T1
Valid prediction for snap_scaffold_9-snap.1791-T1
Couldn't classify 24066, 24503
Sorry, prediction pasa_asmbl_55109.p1 fails validation.
(ATT)	 CC	24066-24503	CC	AAC
Valid prediction for GlimmerHMM_glimmerT_23092-T1
Valid prediction for GeneMark_model.39560_t
Valid prediction for GeneMark_model.39538_t
Valid prediction for GlimmerHMM_glimmerT_23082-T1
Valid prediction for GlimmerHMM_glimmerT_23078-T1
Valid prediction for GeneMark_model.39559_t
Valid prediction for GeneMark_model.39557_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 227444, rend_intergenic: 225151  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 244149, rend_intergenic: 242754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 247735
-exon list size: 301


building trellis

0.3    
0.7    
1.0    
1.3    
1.7    
2.0    
2.3    
2.6    
3.0    
3.3    
3.6    
4.0    
4.3    
4.6    
5.0    
5.3    
5.6    
5.9    
6.3    
6.6    
6.9    
7.3    
7.6    
7.9    
8.3    
8.6    
8.9    
9.2    
9.6    
9.9    
10.2    
10.6    
10.9    
11.2    
11.6    
11.9    
12.2    
12.5    
12.9    
13.2    
13.5    
13.9    
14.2    
14.5    
14.9    
15.2    
15.5    
15.8    
16.2    
16.5    
16.8    
17.2    
17.5    
17.8    
18.2    
18.5    
18.8    
19.1    
19.5    
19.8    
20.1    
20.5    
20.8    
21.1    
21.5    
21.8    
22.1    
22.4    
22.8    
23.1    
23.4    
23.8    
24.1    
24.4    
24.8    
25.1    
25.4    
25.7    
26.1    
26.4    
26.7    
27.1    
27.4    
27.7    
28.1    
28.4    
28.7    
29.0    
29.4    
29.7    
30.0    
30.4    
30.7    
31.0    
31.4    
31.7    
32.0    
32.3    
32.7    
33.0    
33.3    
33.7    
34.0    
34.3    
34.7    
35.0    
35.3    
35.6    
36.0    
36.3    
36.6    
37.0    
37.3    
37.6    
38.0    
38.3    
38.6    
38.9    
39.3    
39.6    
39.9    
40.3    
40.6    
40.9    
41.3    
41.6    
41.9    
42.2    
42.6    
42.9    
43.2    
43.6    
43.9    
44.2    
44.6    
44.9    
45.2    
45.5    
45.9    
46.2    
46.5    
46.9    
47.2    
47.5    
47.9    
48.2    
48.5    
48.8    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.2    
51.5    
51.8    
52.1    
52.5    
52.8    
53.1    
53.5    
53.8    
54.1    
54.5    
54.8    
55.1    
55.4    
55.8    
56.1    
56.4    
56.8    
57.1    
57.4    
57.8    
58.1    
58.4    
58.7    
59.1    
59.4    
59.7    
60.1    
60.4    
60.7    
61.1    
61.4    
61.7    
62.0    
62.4    
62.7    
63.0    
63.4    
63.7    
64.0    
64.4    
64.7    
65.0    
65.3    
65.7    
66.0    
66.3    
66.7    
67.0    
67.3    
67.7    
68.0    
68.3    
68.6    
69.0    
69.3    
69.6    
70.0    
70.3    
70.6    
71.0    
71.3    
71.6    
71.9    
72.3    
72.6    
72.9    
73.3    
73.6    
73.9    
74.3    
74.6    
74.9    
75.2    
75.6    
75.9    
76.2    
76.6    
76.9    
77.2    
77.6    
77.9    
78.2    
78.5    
78.9    
79.2    
79.5    
79.9    
80.2    
80.5    
80.9    
81.2    
81.5    
81.8    
82.2    
82.5    
82.8    
83.2    
83.5    
83.8    
84.2    
84.5    
84.8    
85.1    
85.5    
85.8    
86.1    
86.5    
86.8    
87.1    
87.5    
87.8    
88.1    
88.4    
88.8    
89.1    
89.4    
89.8    
90.1    
90.4    
90.8    
91.1    
91.4    
91.7    
92.1    
92.4    
92.7    
93.1    
93.4    
93.7    
94.1    
94.4    
94.7    
95.0    
95.4    
95.7    
96.0    
96.4    
96.7    
97.0    
97.4    
97.7    
98.0    
98.3    
98.7    
99.0    
99.3    
99.7    
-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 227444, rend_intergenic: 225151  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 244149, rend_intergenic: 242754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 30395
-exon list size: 9


building trellis

9.1    
18.2    
27.3    
36.4    
45.5    
54.5    
63.6    
72.7    
81.8    
90.9    
-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 1 - 28339
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-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 7661 - 28339
-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 7661 - 27387
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-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 7661 - 25527
-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

-building DP trellis

-building trellis in range 7661 - 20494
-exon list size: 1


building trellis

33.3    
66.7    
-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