-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_13879853-14184982

-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 pasa_asmbl_43177.p1
Valid prediction for GeneMark_model.17530_t
Valid prediction for GlimmerHMM_glimmerT_10774-T1
Valid prediction for GeneMark_model.17523_t
Valid prediction for HiQ_model.g7112.t1
Valid prediction for GeneMark_model.17529_t
Valid prediction for HiQ_model.g7101.t1
Valid prediction for GlimmerHMM_glimmerT_10769-T1
Valid prediction for snap_scaffold_4-snap.2880-T1
Valid prediction for CodingQuarry_transcript_49114-T1
Valid prediction for CodingQuarry_transcript_49110-T1
Valid prediction for GeneMark_model.17519_t
Valid prediction for GlimmerHMM_glimmerT_10782-T1
Valid prediction for HiQ_model.g7113.t1
Valid prediction for snap_scaffold_4-snap.2847-T1
Valid prediction for GlimmerHMM_glimmerT_10771-T1
Valid prediction for CodingQuarry_transcript_49112-T1
Couldn't classify 113621, 113634
Sorry, prediction pasa_asmbl_43167.p1 fails validation.
(TTA)	 AA	113621-113634	GT	GAG
(GTA)	 AG	113798-113982	GT	AGG
(GTA)	 AG	114194-114306	CC	AAC
-recovered pasa_asmbl_43167.p1, terminal, 114194, 114306
-recovered pasa_asmbl_43167.p1, internal, 113798, 113982
Valid prediction for CodingQuarry_transcript_49113-T1
Valid prediction for snap_scaffold_4-snap.2867-T1
Couldn't classify 237263, 237319
Sorry, prediction pasa_asmbl_43187.p1 fails validation.
(CAT)	 AA	237263-237319	GT	CTG
(ATG)	 AG	237455-237762	GT	AGG
(AAT)	 AG	237959-238139	TG	GAT
-recovered pasa_asmbl_43187.p1, initial, 237455, 237762
-recovered pasa_asmbl_43187.p1, terminal, 237959, 238139
-recovered pasa_asmbl_43187.p1, internal, 237455, 237762
Valid prediction for HiQ_model.g7106.t1
Valid prediction for snap_scaffold_4-snap.2875-T1
Valid prediction for GeneMark_model.17512_t
Valid prediction for GlimmerHMM_glimmerT_10785-T1
Valid prediction for pasa_asmbl_43171.p1
Valid prediction for snap_scaffold_4-snap.2876-T1
Valid prediction for GlimmerHMM_glimmerT_10783-T1
Valid prediction for snap_scaffold_4-snap.2849-T1
Valid prediction for GlimmerHMM_glimmerT_10784-T1
Valid prediction for HiQ_model.g7111.t1
Couldn't classify 205935, 206547
Sorry, prediction pasa_asmbl_43172.p1 fails validation.
(CAA)	 GT	205935-206547	GT	AGG
(GTA)	 AG	206902-207152	GT	GGG
(GAG)	 AG	207268-207384	AC	GAA
-recovered pasa_asmbl_43172.p1, terminal, 207268, 207384
-recovered pasa_asmbl_43172.p1, internal, 206902, 207152
Valid prediction for GeneMark_model.17522_t
Valid prediction for CodingQuarry_transcript_49111-T1
Valid prediction for GeneMark_model.17509_t
Valid prediction for snap_scaffold_4-snap.2866-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g7096.t1
Valid prediction for snap_scaffold_4-snap.2860-T1
Valid prediction for snap_scaffold_4-snap.2877-T1
Couldn't classify 6571, 7293
Sorry, prediction pasa_asmbl_41768.p1 fails validation.
(GTT)	 CC	6571-7293	TA	AAT
Valid prediction for GlimmerHMM_glimmerT_10763-T1
Valid prediction for snap_scaffold_4-snap.2874-T1
Valid prediction for pasa_asmbl_43168.p1
Valid prediction for Augustus_model.g7095.t1
Valid prediction for HiQ_model.g7115.t1
Valid prediction for GlimmerHMM_glimmerT_10779-T1
Valid prediction for GeneMark_model.17516_t
Valid prediction for snap_scaffold_4-snap.2853-T1
Valid prediction for snap_scaffold_4-snap.2865-T1
Valid prediction for GeneMark_model.17528_t
Valid prediction for snap_scaffold_4-snap.2857-T1
Valid prediction for HiQ_model.g7107.t1
Valid prediction for GlimmerHMM_glimmerT_10778-T1
Valid prediction for GlimmerHMM_glimmerT_10768-T1
Valid prediction for pasa_asmbl_43170.p1
Valid prediction for Augustus_model.g7098.t1
Valid prediction for GeneMark_model.17526_t
Valid prediction for GeneMark_model.17506_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 GlimmerHMM_glimmerT_10762-T1
Valid prediction for HiQ_model.g7102.t1
Valid prediction for GlimmerHMM_glimmerT_10789-T1
Valid prediction for CodingQuarry_transcript_49107-T1
Valid prediction for snap_scaffold_4-snap.2864-T1
Valid prediction for GlimmerHMM_glimmerT_10790-T1
Valid prediction for snap_scaffold_4-snap.2846-T1
Valid prediction for pasa_asmbl_41776.p1
Valid prediction for snap_scaffold_4-snap.2871-T1
Valid prediction for GlimmerHMM_glimmerT_10777-T1
Valid prediction for CodingQuarry_transcript_49106-T1
Valid prediction for GlimmerHMM_glimmerT_10765-T1
Valid prediction for GlimmerHMM_glimmerT_10767-T1
Valid prediction for snap_scaffold_4-snap.2858-T1
Valid prediction for snap_scaffold_4-snap.2848-T1
Valid prediction for snap_scaffold_4-snap.2851-T1
Valid prediction for snap_scaffold_4-snap.2861-T1
Valid prediction for snap_scaffold_4-snap.2859-T1
Valid prediction for Augustus_model.g7110.t1
Valid prediction for Augustus_model.g7108.t1
Valid prediction for Augustus_model.g7105.t1
Valid prediction for HiQ_model.g7116.t1
Valid prediction for GlimmerHMM_glimmerT_10788-T1
Valid prediction for GeneMark_model.17525_t
Valid prediction for snap_scaffold_4-snap.2862-T1
Valid prediction for snap_scaffold_4-snap.2855-T1
Valid prediction for snap_scaffold_4-snap.2863-T1
Valid prediction for snap_scaffold_4-snap.2872-T1
Valid prediction for HiQ_model.g7094.t1
Valid prediction for GlimmerHMM_glimmerT_10775-T1
Valid prediction for GeneMark_model.17515_t
Valid prediction for snap_scaffold_4-snap.2856-T1
Valid prediction for GlimmerHMM_glimmerT_10770-T1
Valid prediction for GlimmerHMM_glimmerT_10773-T1
Valid prediction for GeneMark_model.17527_t
Valid prediction for Augustus_model.g7097.t1
Valid prediction for GeneMark_model.17533_t
Valid prediction for CodingQuarry_transcript_49108-T1
Valid prediction for pasa_asmbl_41770.p1
Valid prediction for GlimmerHMM_glimmerT_10772-T1
Valid prediction for Augustus_model.g7103.t1
Valid prediction for snap_scaffold_4-snap.2854-T1
Valid prediction for GeneMark_model.17508_t
Valid prediction for GeneMark_model.17507_t
Valid prediction for GeneMark_model.17505_t
Valid prediction for GlimmerHMM_glimmerT_10780-T1
Valid prediction for GlimmerHMM_glimmerT_10764-T1
Valid prediction for GlimmerHMM_glimmerT_10781-T1
Valid prediction for snap_scaffold_4-snap.2850-T1
Valid prediction for Augustus_model.g7093.t1
Valid prediction for GeneMark_model.17520_t
Valid prediction for Augustus_model.g7099.t1
Valid prediction for snap_scaffold_4-snap.2879-T1
Valid prediction for GeneMark_model.17511_t
Valid prediction for snap_scaffold_4-snap.2869-T1
Valid prediction for GeneMark_model.17531_t
Valid prediction for GlimmerHMM_glimmerT_10766-T1
Valid prediction for GlimmerHMM_glimmerT_10786-T1
Valid prediction for snap_scaffold_4-snap.2870-T1
Valid prediction for snap_scaffold_4-snap.2873-T1
Couldn't classify 64671, 64850
Sorry, prediction pasa_asmbl_41780.p1 fails validation.
(AAA)	 CT	64671-64850	GT	AGG
(GTG)	 AG	65016-65258	GT	GAG
-recovered pasa_asmbl_41780.p1, terminal, 65016, 65258
-recovered pasa_asmbl_41780.p1, internal, 65016, 65258
Valid prediction for GeneMark_model.17518_t
Valid prediction for GeneMark_model.17532_t
Valid prediction for HiQ_model.g7114.t1
Valid prediction for snap_scaffold_4-snap.2878-T1
Valid prediction for GeneMark_model.17514_t
Valid prediction for GlimmerHMM_glimmerT_10776-T1
Valid prediction for GlimmerHMM_glimmerT_10787-T1
Valid prediction for GlimmerHMM_glimmerT_10761-T1
Valid prediction for Augustus_model.g7109.t1
Valid prediction for GeneMark_model.17513_t
Valid prediction for GeneMark_model.17524_t
Valid prediction for Augustus_model.g7117.t1
Valid prediction for Augustus_model.g7104.t1
Valid prediction for snap_scaffold_4-snap.2852-T1
Valid prediction for HiQ_model.g7100.t1
Valid prediction for snap_scaffold_4-snap.2868-T1
Valid prediction for GeneMark_model.17517_t
Valid prediction for GeneMark_model.17510_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13277, rend_intergenic: 8197  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 305130
-exon list size: 420


building trellis

0.2    
0.5    
0.7    
0.9    
1.2    
1.4    
1.7    
1.9    
2.1    
2.4    
2.6    
2.8    
3.1    
3.3    
3.6    
3.8    
4.0    
4.3    
4.5    
4.7    
5.0    
5.2    
5.5    
5.7    
5.9    
6.2    
6.4    
6.6    
6.9    
7.1    
7.3    
7.6    
7.8    
8.1    
8.3    
8.5    
8.8    
9.0    
9.2    
9.5    
9.7    
10.0    
10.2    
10.4    
10.7    
10.9    
11.1    
11.4    
11.6    
11.8    
12.1    
12.3    
12.6    
12.8    
13.0    
13.3    
13.5    
13.7    
14.0    
14.2    
14.5    
14.7    
14.9    
15.2    
15.4    
15.6    
15.9    
16.1    
16.4    
16.6    
16.8    
17.1    
17.3    
17.5    
17.8    
18.0    
18.2    
18.5    
18.7    
19.0    
19.2    
19.4    
19.7    
19.9    
20.1    
20.4    
20.6    
20.9    
21.1    
21.3    
21.6    
21.8    
22.0    
22.3    
22.5    
22.7    
23.0    
23.2    
23.5    
23.7    
23.9    
24.2    
24.4    
24.6    
24.9    
25.1    
25.4    
25.6    
25.8    
26.1    
26.3    
26.5    
26.8    
27.0    
27.3    
27.5    
27.7    
28.0    
28.2    
28.4    
28.7    
28.9    
29.1    
29.4    
29.6    
29.9    
30.1    
30.3    
30.6    
30.8    
31.0    
31.3    
31.5    
31.8    
32.0    
32.2    
32.5    
32.7    
32.9    
33.2    
33.4    
33.6    
33.9    
34.1    
34.4    
34.6    
34.8    
35.1    
35.3    
35.5    
35.8    
36.0    
36.3    
36.5    
36.7    
37.0    
37.2    
37.4    
37.7    
37.9    
38.2    
38.4    
38.6    
38.9    
39.1    
39.3    
39.6    
39.8    
40.0    
40.3    
40.5    
40.8    
41.0    
41.2    
41.5    
41.7    
41.9    
42.2    
42.4    
42.7    
42.9    
43.1    
43.4    
43.6    
43.8    
44.1    
44.3    
44.5    
44.8    
45.0    
45.3    
45.5    
45.7    
46.0    
46.2    
46.4    
46.7    
46.9    
47.2    
47.4    
47.6    
47.9    
48.1    
48.3    
48.6    
48.8    
49.1    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
50.9    
51.2    
51.4    
51.7    
51.9    
52.1    
52.4    
52.6    
52.8    
53.1    
53.3    
53.6    
53.8    
54.0    
54.3    
54.5    
54.7    
55.0    
55.2    
55.5    
55.7    
55.9    
56.2    
56.4    
56.6    
56.9    
57.1    
57.3    
57.6    
57.8    
58.1    
58.3    
58.5    
58.8    
59.0    
59.2    
59.5    
59.7    
60.0    
60.2    
60.4    
60.7    
60.9    
61.1    
61.4    
61.6    
61.8    
62.1    
62.3    
62.6    
62.8    
63.0    
63.3    
63.5    
63.7    
64.0    
64.2    
64.5    
64.7    
64.9    
65.2    
65.4    
65.6    
65.9    
66.1    
66.4    
66.6    
66.8    
67.1    
67.3    
67.5    
67.8    
68.0    
68.2    
68.5    
68.7    
69.0    
69.2    
69.4    
69.7    
69.9    
70.1    
70.4    
70.6    
70.9    
71.1    
71.3    
71.6    
71.8    
72.0    
72.3    
72.5    
72.7    
73.0    
73.2    
73.5    
73.7    
73.9    
74.2    
74.4    
74.6    
74.9    
75.1    
75.4    
75.6    
75.8    
76.1    
76.3    
76.5    
76.8    
77.0    
77.3    
77.5    
77.7    
78.0    
78.2    
78.4    
78.7    
78.9    
79.1    
79.4    
79.6    
79.9    
80.1    
80.3    
80.6    
80.8    
81.0    
81.3    
81.5    
81.8    
82.0    
82.2    
82.5    
82.7    
82.9    
83.2    
83.4    
83.6    
83.9    
84.1    
84.4    
84.6    
84.8    
85.1    
85.3    
85.5    
85.8    
86.0    
86.3    
86.5    
86.7    
87.0    
87.2    
87.4    
87.7    
87.9    
88.2    
88.4    
88.6    
88.9    
89.1    
89.3    
89.6    
89.8    
90.0    
90.3    
90.5    
90.8    
91.0    
91.2    
91.5    
91.7    
91.9    
92.2    
92.4    
92.7    
92.9    
93.1    
93.4    
93.6    
93.8    
94.1    
94.3    
94.5    
94.8    
95.0    
95.3    
95.5    
95.7    
96.0    
96.2    
96.4    
96.7    
96.9    
97.2    
97.4    
97.6    
97.9    
98.1    
98.3    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 13277, rend_intergenic: 8197  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 30 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 253705 - 305130
-exon list size: 17


building trellis

5.3    
10.5    
15.8    
21.1    
26.3    
31.6    
36.8    
42.1    
47.4    
52.6    
57.9    
63.2    
68.4    
73.7    
78.9    
84.2    
89.5    
94.7    
-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 254664 - 305130
-exon list size: 15


building trellis

5.9    
11.8    
17.6    
23.5    
29.4    
35.3    
41.2    
47.1    
52.9    
58.8    
64.7    
70.6    
76.5    
82.4    
88.2    
94.1    
-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 254664 - 269915
-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
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 256761 - 269915
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-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

-building DP trellis

-building trellis in range 256761 - 269761
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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 269934 - 305130
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-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 270146 - 305130
-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 270146 - 280591
-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

-building DP trellis

-building trellis in range 280624 - 305130
-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 280624 - 291384
-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

-building DP trellis

-building trellis in range 291473 - 305130
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal

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