-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_15/scaffold_15_14772606-15006592

-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_15-snap.2960-T1
Valid prediction for snap_scaffold_15-snap.2955-T1
Valid prediction for GlimmerHMM_glimmerT_38258-T1
Valid prediction for snap_scaffold_15-snap.2961-T1
Valid prediction for GlimmerHMM_glimmerT_38240-T1
Valid prediction for snap_scaffold_15-snap.2977-T1
Valid prediction for Augustus_model.g25668.t1
Valid prediction for GeneMark_model.65691_t
Valid prediction for GeneMark_model.65711_t
Valid prediction for snap_scaffold_15-snap.2978-T1
Valid prediction for GeneMark_model.65689_t
Valid prediction for CodingQuarry_transcript_18200-T1
Valid prediction for snap_scaffold_15-snap.2966-T1
Valid prediction for GlimmerHMM_glimmerT_38238-T1
Valid prediction for snap_scaffold_15-snap.2958-T1
Valid prediction for GlimmerHMM_glimmerT_38232-T1
Valid prediction for GeneMark_model.65687_t
Valid prediction for Augustus_model.g25652.t1
Valid prediction for GlimmerHMM_glimmerT_38244-T1
Valid prediction for GeneMark_model.65693_t
Valid prediction for snap_scaffold_15-snap.2976-T1
Valid prediction for snap_scaffold_15-snap.2953-T1
Valid prediction for Augustus_model.g25661.t1
Valid prediction for GeneMark_model.65701_t
Valid prediction for GlimmerHMM_glimmerT_38241-T1
Valid prediction for GlimmerHMM_glimmerT_38252-T1
Valid prediction for GeneMark_model.65705_t
Valid prediction for snap_scaffold_15-snap.2971-T1
Valid prediction for GeneMark_model.65697_t
Valid prediction for GeneMark_model.65707_t
Valid prediction for pasa_asmbl_14653.p1
Valid prediction for GlimmerHMM_glimmerT_38237-T1
Valid prediction for Augustus_model.g25653.t1
Valid prediction for snap_scaffold_15-snap.2987-T1
Valid prediction for snap_scaffold_15-snap.2963-T1
Valid prediction for GeneMark_model.65698_t
Valid prediction for GeneMark_model.65685_t
Valid prediction for HiQ_model.g25660.t1
Valid prediction for snap_scaffold_15-snap.2973-T1
Valid prediction for Augustus_model.g25656.t1
Valid prediction for GlimmerHMM_glimmerT_38247-T1
Valid prediction for Augustus_model.g25654.t1
Valid prediction for CodingQuarry_transcript_18201-T1
Valid prediction for snap_scaffold_15-snap.2965-T1
Valid prediction for GeneMark_model.65695_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 GeneMark_model.65694_t
Valid prediction for Augustus_model.g25667.t1
Valid prediction for GeneMark_model.65710_t
Valid prediction for Augustus_model.g25655.t1
Valid prediction for Augustus_model.g25665.t1
Valid prediction for GeneMark_model.65703_t
Valid prediction for GlimmerHMM_glimmerT_38253-T1
Valid prediction for GeneMark_model.65708_t
Valid prediction for GeneMark_model.65690_t
Valid prediction for snap_scaffold_15-snap.2980-T1
Valid prediction for snap_scaffold_15-snap.2967-T1
Couldn't classify 146550, 146610
Sorry, prediction pasa_asmbl_15768.p1 fails validation.
(ATG)	 AA	143829-143948	GT	AGG
(GCA)	 AG	145391-145454	GT	AGG
(AGG)	 AG	145737-145846	GT	ATG
(AAA)	 AG	146056-146172	GT	CAG
(GAA)	 AG	146342-146400	GT	AGG
(GTT)	 AG	146550-146610	CT	AGC
-recovered pasa_asmbl_15768.p1, initial, 143829, 143948
-recovered pasa_asmbl_15768.p1, internal, 145391, 145454
-recovered pasa_asmbl_15768.p1, internal, 145737, 145846
-recovered pasa_asmbl_15768.p1, internal, 146056, 146172
-recovered pasa_asmbl_15768.p1, internal, 146342, 146400
Valid prediction for GlimmerHMM_glimmerT_38235-T1
Valid prediction for GlimmerHMM_glimmerT_38239-T1
Valid prediction for snap_scaffold_15-snap.2979-T1
Valid prediction for snap_scaffold_15-snap.2981-T1
Valid prediction for GlimmerHMM_glimmerT_38242-T1
Valid prediction for Augustus_model.g25664.t1
Valid prediction for snap_scaffold_15-snap.2989-T1
Valid prediction for Augustus_model.g25659.t1
Valid prediction for GeneMark_model.65686_t
Valid prediction for GlimmerHMM_glimmerT_38255-T1
Valid prediction for GlimmerHMM_glimmerT_38246-T1
Valid prediction for Augustus_model.g25651.t1
Valid prediction for snap_scaffold_15-snap.2988-T1
Valid prediction for HiQ_model.g25657.t1
Valid prediction for snap_scaffold_15-snap.2968-T1
Valid prediction for Augustus_model.g25662.t1
Valid prediction for GlimmerHMM_glimmerT_38256-T1
Valid prediction for GeneMark_model.65688_t
Valid prediction for snap_scaffold_15-snap.2956-T1
Valid prediction for snap_scaffold_15-snap.2985-T1
Valid prediction for snap_scaffold_15-snap.2957-T1
Valid prediction for GeneMark_model.65702_t
Valid prediction for snap_scaffold_15-snap.2952-T1
Valid prediction for snap_scaffold_15-snap.2964-T1
Valid prediction for GeneMark_model.65706_t
Valid prediction for GlimmerHMM_glimmerT_38251-T1
Valid prediction for snap_scaffold_15-snap.2982-T1
Couldn't classify 146801, 146871
Sorry, prediction pasa_asmbl_15766.p1 fails validation.
(GAA)	 AG	146801-146871	GT	AAG
(TTT)	 AG	147605-147709	GT	ATG
(GTT)	 AG	148110-148253	GT	AGG
(GAT)	 AG	148424-148581	GT	CTG
(TTG)	 AG	148754-148830	AT	AAA
-recovered pasa_asmbl_15766.p1, terminal, 148754, 148830
-recovered pasa_asmbl_15766.p1, internal, 146801, 146871
-recovered pasa_asmbl_15766.p1, internal, 147605, 147709
-recovered pasa_asmbl_15766.p1, internal, 148110, 148253
-recovered pasa_asmbl_15766.p1, internal, 148424, 148581
Valid prediction for snap_scaffold_15-snap.2969-T1
Valid prediction for snap_scaffold_15-snap.2962-T1
Valid prediction for snap_scaffold_15-snap.2954-T1
Valid prediction for snap_scaffold_15-snap.2972-T1
Valid prediction for GlimmerHMM_glimmerT_38249-T1
Valid prediction for GlimmerHMM_glimmerT_38254-T1
Valid prediction for GlimmerHMM_glimmerT_38248-T1
Valid prediction for GeneMark_model.65696_t
Valid prediction for snap_scaffold_15-snap.2970-T1
Valid prediction for GlimmerHMM_glimmerT_38234-T1
Valid prediction for GlimmerHMM_glimmerT_38243-T1
Valid prediction for GlimmerHMM_glimmerT_38233-T1
Valid prediction for snap_scaffold_15-snap.2984-T1
Valid prediction for GeneMark_model.65709_t
Valid prediction for GlimmerHMM_glimmerT_38250-T1
Valid prediction for snap_scaffold_15-snap.2986-T1
Valid prediction for GeneMark_model.65692_t
Valid prediction for snap_scaffold_15-snap.2975-T1
Valid prediction for GeneMark_model.65704_t
Valid prediction for Augustus_model.g25663.t1
Valid prediction for Augustus_model.g25650.t1
Valid prediction for GlimmerHMM_glimmerT_38245-T1
Valid prediction for snap_scaffold_15-snap.2983-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_38257-T1
Valid prediction for Augustus_model.g25658.t1
Valid prediction for snap_scaffold_15-snap.2974-T1
Valid prediction for Augustus_model.g25666.t1
Valid prediction for snap_scaffold_15-snap.2959-T1
Valid prediction for GeneMark_model.65699_t
Valid prediction for GlimmerHMM_glimmerT_38236-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11168, rend_intergenic: 6933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21467, rend_intergenic: 17620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44200, rend_intergenic: 40525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53025, rend_intergenic: 50019  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101407, rend_intergenic: 99341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104656, rend_intergenic: 101989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108227, rend_intergenic: 106271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 233987
-exon list size: 427


building trellis

0.2    
0.5    
0.7    
0.9    
1.2    
1.4    
1.6    
1.9    
2.1    
2.3    
2.6    
2.8    
3.0    
3.3    
3.5    
3.7    
4.0    
4.2    
4.4    
4.7    
4.9    
5.1    
5.4    
5.6    
5.8    
6.1    
6.3    
6.5    
6.8    
7.0    
7.2    
7.5    
7.7    
7.9    
8.2    
8.4    
8.6    
8.9    
9.1    
9.3    
9.6    
9.8    
10.0    
10.3    
10.5    
10.7    
11.0    
11.2    
11.4    
11.7    
11.9    
12.1    
12.4    
12.6    
12.8    
13.1    
13.3    
13.5    
13.8    
14.0    
14.2    
14.5    
14.7    
14.9    
15.2    
15.4    
15.6    
15.9    
16.1    
16.3    
16.6    
16.8    
17.0    
17.2    
17.5    
17.7    
17.9    
18.2    
18.4    
18.6    
18.9    
19.1    
19.3    
19.6    
19.8    
20.0    
20.3    
20.5    
20.7    
21.0    
21.2    
21.4    
21.7    
21.9    
22.1    
22.4    
22.6    
22.8    
23.1    
23.3    
23.5    
23.8    
24.0    
24.2    
24.5    
24.7    
24.9    
25.2    
25.4    
25.6    
25.9    
26.1    
26.3    
26.6    
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    
29.8    
30.1    
30.3    
30.5    
30.8    
31.0    
31.2    
31.5    
31.7    
31.9    
32.2    
32.4    
32.6    
32.9    
33.1    
33.3    
33.6    
33.8    
34.0    
34.3    
34.5    
34.7    
35.0    
35.2    
35.4    
35.7    
35.9    
36.1    
36.4    
36.6    
36.8    
37.1    
37.3    
37.5    
37.8    
38.0    
38.2    
38.5    
38.7    
38.9    
39.2    
39.4    
39.6    
39.9    
40.1    
40.3    
40.6    
40.8    
41.0    
41.3    
41.5    
41.7    
42.0    
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    
45.2    
45.5    
45.7    
45.9    
46.2    
46.4    
46.6    
46.9    
47.1    
47.3    
47.6    
47.8    
48.0    
48.3    
48.5    
48.7    
49.0    
49.2    
49.4    
49.7    
49.9    
50.1    
50.3    
50.6    
50.8    
51.0    
51.3    
51.5    
51.7    
52.0    
52.2    
52.4    
52.7    
52.9    
53.1    
53.4    
53.6    
53.8    
54.1    
54.3    
54.5    
54.8    
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    
58.0    
58.3    
58.5    
58.7    
59.0    
59.2    
59.4    
59.7    
59.9    
60.1    
60.4    
60.6    
60.8    
61.1    
61.3    
61.5    
61.8    
62.0    
62.2    
62.5    
62.7    
62.9    
63.2    
63.4    
63.6    
63.9    
64.1    
64.3    
64.6    
64.8    
65.0    
65.3    
65.5    
65.7    
66.0    
66.2    
66.4    
66.7    
66.9    
67.1    
67.4    
67.6    
67.8    
68.1    
68.3    
68.5    
68.8    
69.0    
69.2    
69.5    
69.7    
69.9    
70.2    
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    
73.4    
73.7    
73.9    
74.1    
74.4    
74.6    
74.8    
75.1    
75.3    
75.5    
75.8    
76.0    
76.2    
76.5    
76.7    
76.9    
77.2    
77.4    
77.6    
77.9    
78.1    
78.3    
78.6    
78.8    
79.0    
79.3    
79.5    
79.7    
80.0    
80.2    
80.4    
80.7    
80.9    
81.1    
81.4    
81.6    
81.8    
82.1    
82.3    
82.5    
82.8    
83.0    
83.2    
83.4    
83.7    
83.9    
84.1    
84.4    
84.6    
84.8    
85.1    
85.3    
85.5    
85.8    
86.0    
86.2    
86.5    
86.7    
86.9    
87.2    
87.4    
87.6    
87.9    
88.1    
88.3    
88.6    
88.8    
89.0    
89.3    
89.5    
89.7    
90.0    
90.2    
90.4    
90.7    
90.9    
91.1    
91.4    
91.6    
91.8    
92.1    
92.3    
92.5    
92.8    
93.0    
93.2    
93.5    
93.7    
93.9    
94.2    
94.4    
94.6    
94.9    
95.1    
95.3    
95.6    
95.8    
96.0    
96.3    
96.5    
96.7    
97.0    
97.2    
97.4    
97.7    
97.9    
98.1    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 11168, rend_intergenic: 6933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21467, rend_intergenic: 17620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44200, rend_intergenic: 40525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53025, rend_intergenic: 50019  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101407, rend_intergenic: 99341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104656, rend_intergenic: 101989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108227, rend_intergenic: 106271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 216066 - 233987
-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 216066 - 228445
-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 216187 - 228445
-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 216187 - 228200
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-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 216187 - 228117
-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 216187 - 227657
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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