-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_15/scaffold_15_12704568-12935785

-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_37989-T1
Valid prediction for GeneMark_model.65285_t
Valid prediction for Augustus_model.g25458.t1
Valid prediction for snap_scaffold_15-snap.2585-T1
Valid prediction for GlimmerHMM_glimmerT_37968-T1
Valid prediction for Augustus_model.g25448.t1
Valid prediction for GeneMark_model.65300_t
Valid prediction for CodingQuarry_transcript_18144-T1
Valid prediction for GeneMark_model.65288_t
Valid prediction for GlimmerHMM_glimmerT_37980-T1
Valid prediction for GeneMark_model.65312_t
Valid prediction for snap_scaffold_15-snap.2587-T1
Valid prediction for GlimmerHMM_glimmerT_37973-T1
Valid prediction for snap_scaffold_15-snap.2583-T1
Couldn't classify 71785, 71851
Couldn't classify 82931, 82982
Sorry, prediction pasa_asmbl_14550.p1 fails validation.
(GTC)	 CA	71785-71851	GT	AGG
(GGG)	 AG	72070-72140	GT	AGG
(ATT)	 AG	74821-74877	GT	AGG
(GCA)	 AG	75618-75854	GT	AGG
(GAG)	 AG	76396-76515	GT	AGG
(CAA)	 AG	77226-77325	GT	AGG
(ACA)	 AG	78329-78441	GT	AGG
(CTG)	 AG	79105-79255	GT	AGG
(CCG)	 AG	79443-79642	GT	CGG
(AGT)	 AG	80184-80287	GT	AGG
(CAC)	 AG	82931-82982	AT	GCA
add_exon() Sorry, pasa_asmbl_14550.p1 77226-77325-terminal-3 is invalid.
-recovered pasa_asmbl_14550.p1, terminal, 77226, 77325
-recovered pasa_asmbl_14550.p1, internal, 72070, 72140
-recovered pasa_asmbl_14550.p1, internal, 74821, 74877
-recovered pasa_asmbl_14550.p1, internal, 75618, 75854
-recovered pasa_asmbl_14550.p1, internal, 76396, 76515
-recovered pasa_asmbl_14550.p1, internal, 77226, 77325
-recovered pasa_asmbl_14550.p1, internal, 78329, 78441
-recovered pasa_asmbl_14550.p1, internal, 79105, 79255
-recovered pasa_asmbl_14550.p1, internal, 79443, 79642
-recovered pasa_asmbl_14550.p1, internal, 80184, 80287
Valid prediction for GeneMark_model.65298_t
Valid prediction for snap_scaffold_15-snap.2584-T1
Valid prediction for GeneMark_model.65310_t
Valid prediction for snap_scaffold_15-snap.2605-T1
Valid prediction for GlimmerHMM_glimmerT_37963-T1
Valid prediction for CodingQuarry_transcript_18145-T1
Valid prediction for Augustus_model.g25453.t1
Valid prediction for Augustus_model.g25456.t1
Valid prediction for GeneMark_model.65293_t
Valid prediction for GeneMark_model.65297_t
Valid prediction for Augustus_model.g25455.t1
Valid prediction for HiQ_model.g25451.t1
Valid prediction for GeneMark_model.65295_t
Valid prediction for HiQ_model.g25452.t1
Valid prediction for GlimmerHMM_glimmerT_37971-T1
Valid prediction for GlimmerHMM_glimmerT_37962-T1
Valid prediction for GlimmerHMM_glimmerT_37990-T1
Valid prediction for snap_scaffold_15-snap.2581-T1
Valid prediction for GlimmerHMM_glimmerT_37966-T1
Valid prediction for snap_scaffold_15-snap.2596-T1
Valid prediction for Augustus_model.g25465.t1
Valid prediction for GeneMark_model.65286_t
Valid prediction for snap_scaffold_15-snap.2601-T1
Valid prediction for pasa_asmbl_14540.p1
Valid prediction for snap_scaffold_15-snap.2592-T1
Couldn't classify 84300, 84316
Sorry, prediction pasa_asmbl_14553.p1 fails validation.
(TTC)	 CA	84300-84316	GT	AGG
(AGG)	 AG	86508-86552	GT	AGG
(TCG)	 AG	87520-87910	GG	AGG
-recovered pasa_asmbl_14553.p1, terminal, 87520, 87910
-recovered pasa_asmbl_14553.p1, internal, 86508, 86552
Valid prediction for GlimmerHMM_glimmerT_37985-T1
Valid prediction for snap_scaffold_15-snap.2595-T1
Valid prediction for snap_scaffold_15-snap.2607-T1
Valid prediction for snap_scaffold_15-snap.2598-T1
Valid prediction for GeneMark_model.65314_t
Valid prediction for snap_scaffold_15-snap.2582-T1
Valid prediction for Augustus_model.g25461.t1
Valid prediction for snap_scaffold_15-snap.2589-T1
Valid prediction for Augustus_model.g25450.t1
Valid prediction for GeneMark_model.65315_t
Valid prediction for snap_scaffold_15-snap.2577-T1
Valid prediction for snap_scaffold_15-snap.2591-T1
Valid prediction for GlimmerHMM_glimmerT_37964-T1
Valid prediction for GlimmerHMM_glimmerT_37969-T1
Valid prediction for snap_scaffold_15-snap.2578-T1
Valid prediction for GeneMark_model.65289_t
Valid prediction for GeneMark_model.65291_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_37975-T1
Valid prediction for GeneMark_model.65301_t
Valid prediction for snap_scaffold_15-snap.2608-T1
Valid prediction for GlimmerHMM_glimmerT_37960-T1
Valid prediction for GeneMark_model.65303_t
Valid prediction for GeneMark_model.65296_t
Valid prediction for snap_scaffold_15-snap.2590-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.65309_t
Valid prediction for GlimmerHMM_glimmerT_37972-T1
Valid prediction for Augustus_model.g25462.t1
Valid prediction for GlimmerHMM_glimmerT_37961-T1
Valid prediction for GeneMark_model.65299_t
Valid prediction for GlimmerHMM_glimmerT_37987-T1
Valid prediction for GlimmerHMM_glimmerT_37965-T1
Couldn't classify 140191, 140341
Sorry, prediction pasa_asmbl_15620.p1 fails validation.
(TGG)	 TG	140191-140341	GT	GGG
(GTG)	 AG	140680-140858	AA	GAA
-recovered pasa_asmbl_15620.p1, terminal, 140680, 140858
Valid prediction for snap_scaffold_15-snap.2597-T1
Valid prediction for GlimmerHMM_glimmerT_37986-T1
Valid prediction for Augustus_model.g25467.t1
Valid prediction for snap_scaffold_15-snap.2599-T1
Valid prediction for GeneMark_model.65306_t
Valid prediction for snap_scaffold_15-snap.2593-T1
Valid prediction for GlimmerHMM_glimmerT_37982-T1
Valid prediction for GeneMark_model.65313_t
Valid prediction for GeneMark_model.65304_t
Valid prediction for GlimmerHMM_glimmerT_37984-T1
Valid prediction for snap_scaffold_15-snap.2579-T1
Valid prediction for snap_scaffold_15-snap.2609-T1
Valid prediction for GlimmerHMM_glimmerT_37983-T1
Valid prediction for HiQ_model.g25466.t1
Valid prediction for GlimmerHMM_glimmerT_37970-T1
Valid prediction for snap_scaffold_15-snap.2606-T1
Valid prediction for snap_scaffold_15-snap.2594-T1
Valid prediction for GlimmerHMM_glimmerT_37979-T1
Valid prediction for snap_scaffold_15-snap.2604-T1
Valid prediction for snap_scaffold_15-snap.2580-T1
Valid prediction for Augustus_model.g25460.t1
Valid prediction for GeneMark_model.65307_t
Valid prediction for GlimmerHMM_glimmerT_37988-T1
Valid prediction for HiQ_model.g25457.t1
Valid prediction for GeneMark_model.65308_t
Valid prediction for snap_scaffold_15-snap.2588-T1
Valid prediction for snap_scaffold_15-snap.2603-T1
Valid prediction for GeneMark_model.65294_t
Valid prediction for GeneMark_model.65292_t
Valid prediction for Augustus_model.g25454.t1
Valid prediction for Augustus_model.g25464.t1
Valid prediction for GlimmerHMM_glimmerT_37974-T1
Valid prediction for snap_scaffold_15-snap.2586-T1
Valid prediction for GeneMark_model.65305_t
Valid prediction for snap_scaffold_15-snap.2600-T1
Valid prediction for GeneMark_model.65287_t
Valid prediction for GlimmerHMM_glimmerT_37977-T1
Valid prediction for GeneMark_model.65302_t
Valid prediction for Augustus_model.g25459.t1
Valid prediction for GeneMark_model.65311_t
Valid prediction for GlimmerHMM_glimmerT_37978-T1
Valid prediction for Augustus_model.g25463.t1
Valid prediction for GlimmerHMM_glimmerT_37967-T1
Valid prediction for GlimmerHMM_glimmerT_37981-T1
Valid prediction for Augustus_model.g25449.t1
Valid prediction for snap_scaffold_15-snap.2602-T1
Valid prediction for GlimmerHMM_glimmerT_37976-T1
Valid prediction for GeneMark_model.65290_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11838, rend_intergenic: 9862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70025, rend_intergenic: 63208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70926, rend_intergenic: 70025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72532, rend_intergenic: 71322  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80540, rend_intergenic: 72982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124409, rend_intergenic: 123356  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127754, rend_intergenic: 125070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215761, rend_intergenic: 212397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 231218
-exon list size: 448


building trellis

0.2    
0.4    
0.7    
0.9    
1.1    
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1.6    
1.8    
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2.9    
3.1    
3.3    
3.6    
3.8    
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4.9    
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5.6    
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6.4    
6.7    
6.9    
7.1    
7.3    
7.6    
7.8    
8.0    
8.2    
8.4    
8.7    
8.9    
9.1    
9.3    
9.6    
9.8    
10.0    
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10.4    
10.7    
10.9    
11.1    
11.3    
11.6    
11.8    
12.0    
12.2    
12.4    
12.7    
12.9    
13.1    
13.3    
13.6    
13.8    
14.0    
14.2    
14.4    
14.7    
14.9    
15.1    
15.3    
15.6    
15.8    
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16.9    
17.1    
17.3    
17.6    
17.8    
18.0    
18.2    
18.4    
18.7    
18.9    
19.1    
19.3    
19.6    
19.8    
20.0    
20.2    
20.4    
20.7    
20.9    
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21.3    
21.6    
21.8    
22.0    
22.2    
22.4    
22.7    
22.9    
23.1    
23.3    
23.6    
23.8    
24.0    
24.2    
24.4    
24.7    
24.9    
25.1    
25.3    
25.6    
25.8    
26.0    
26.2    
26.4    
26.7    
26.9    
27.1    
27.3    
27.6    
27.8    
28.0    
28.2    
28.4    
28.7    
28.9    
29.1    
29.3    
29.6    
29.8    
30.0    
30.2    
30.4    
30.7    
30.9    
31.1    
31.3    
31.6    
31.8    
32.0    
32.2    
32.4    
32.7    
32.9    
33.1    
33.3    
33.6    
33.8    
34.0    
34.2    
34.4    
34.7    
34.9    
35.1    
35.3    
35.6    
35.8    
36.0    
36.2    
36.4    
36.7    
36.9    
37.1    
37.3    
37.6    
37.8    
38.0    
38.2    
38.4    
38.7    
38.9    
39.1    
39.3    
39.6    
39.8    
40.0    
40.2    
40.4    
40.7    
40.9    
41.1    
41.3    
41.6    
41.8    
42.0    
42.2    
42.4    
42.7    
42.9    
43.1    
43.3    
43.6    
43.8    
44.0    
44.2    
44.4    
44.7    
44.9    
45.1    
45.3    
45.6    
45.8    
46.0    
46.2    
46.4    
46.7    
46.9    
47.1    
47.3    
47.6    
47.8    
48.0    
48.2    
48.4    
48.7    
48.9    
49.1    
49.3    
49.6    
49.8    
50.0    
50.2    
50.4    
50.7    
50.9    
51.1    
51.3    
51.6    
51.8    
52.0    
52.2    
52.4    
52.7    
52.9    
53.1    
53.3    
53.6    
53.8    
54.0    
54.2    
54.4    
54.7    
54.9    
55.1    
55.3    
55.6    
55.8    
56.0    
56.2    
56.4    
56.7    
56.9    
57.1    
57.3    
57.6    
57.8    
58.0    
58.2    
58.4    
58.7    
58.9    
59.1    
59.3    
59.6    
59.8    
60.0    
60.2    
60.4    
60.7    
60.9    
61.1    
61.3    
61.6    
61.8    
62.0    
62.2    
62.4    
62.7    
62.9    
63.1    
63.3    
63.6    
63.8    
64.0    
64.2    
64.4    
64.7    
64.9    
65.1    
65.3    
65.6    
65.8    
66.0    
66.2    
66.4    
66.7    
66.9    
67.1    
67.3    
67.6    
67.8    
68.0    
68.2    
68.4    
68.7    
68.9    
69.1    
69.3    
69.6    
69.8    
70.0    
70.2    
70.4    
70.7    
70.9    
71.1    
71.3    
71.6    
71.8    
72.0    
72.2    
72.4    
72.7    
72.9    
73.1    
73.3    
73.6    
73.8    
74.0    
74.2    
74.4    
74.7    
74.9    
75.1    
75.3    
75.6    
75.8    
76.0    
76.2    
76.4    
76.7    
76.9    
77.1    
77.3    
77.6    
77.8    
78.0    
78.2    
78.4    
78.7    
78.9    
79.1    
79.3    
79.6    
79.8    
80.0    
80.2    
80.4    
80.7    
80.9    
81.1    
81.3    
81.6    
81.8    
82.0    
82.2    
82.4    
82.7    
82.9    
83.1    
83.3    
83.6    
83.8    
84.0    
84.2    
84.4    
84.7    
84.9    
85.1    
85.3    
85.6    
85.8    
86.0    
86.2    
86.4    
86.7    
86.9    
87.1    
87.3    
87.6    
87.8    
88.0    
88.2    
88.4    
88.7    
88.9    
89.1    
89.3    
89.6    
89.8    
90.0    
90.2    
90.4    
90.7    
90.9    
91.1    
91.3    
91.6    
91.8    
92.0    
92.2    
92.4    
92.7    
92.9    
93.1    
93.3    
93.6    
93.8    
94.0    
94.2    
94.4    
94.7    
94.9    
95.1    
95.3    
95.6    
95.8    
96.0    
96.2    
96.4    
96.7    
96.9    
97.1    
97.3    
97.6    
97.8    
98.0    
98.2    
98.4    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 11838, rend_intergenic: 9862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70025, rend_intergenic: 63208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70926, rend_intergenic: 70025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72532, rend_intergenic: 71322  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80540, rend_intergenic: 72982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124409, rend_intergenic: 123356  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127754, rend_intergenic: 125070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215761, rend_intergenic: 212397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 217802 - 231218
-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 218134 - 231218
-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 218249 - 231218
-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