-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_18353403-18522223

-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_2544-T1
Couldn't classify 6265, 6600
Sorry, prediction pasa_asmbl_2546.p1 fails validation.
(CAC)	 GC	6265-6600	AC	AGA
Valid prediction for GeneMark_model.3765_t
Valid prediction for Augustus_model.g1839.t1
Valid prediction for Augustus_model.g1829.t1
Valid prediction for snap_scaffold_1-snap.3396-T1
Valid prediction for snap_scaffold_1-snap.3370-T1
Valid prediction for GeneMark_model.3741_t
Valid prediction for GeneMark_model.3778_t
Valid prediction for snap_scaffold_1-snap.3386-T1
Valid prediction for Augustus_model.g1835.t1
Valid prediction for snap_scaffold_1-snap.3376-T1
Valid prediction for GeneMark_model.3773_t
Valid prediction for snap_scaffold_1-snap.3389-T1
Valid prediction for GeneMark_model.3755_t
Valid prediction for GeneMark_model.3761_t
Valid prediction for GeneMark_model.3736_t
Valid prediction for snap_scaffold_1-snap.3371-T1
Valid prediction for Augustus_model.g1823.t1
Valid prediction for GlimmerHMM_glimmerT_2537-T1
Valid prediction for GeneMark_model.3740_t
Valid prediction for GlimmerHMM_glimmerT_2546-T1
Valid prediction for snap_scaffold_1-snap.3379-T1
Valid prediction for GlimmerHMM_glimmerT_2545-T1
Valid prediction for snap_scaffold_1-snap.3368-T1
Valid prediction for snap_scaffold_1-snap.3383-T1
Valid prediction for Augustus_model.g1822.t1
Valid prediction for Augustus_model.g1830.t1
Valid prediction for snap_scaffold_1-snap.3374-T1
Valid prediction for CodingQuarry_transcript_2992-T1
Valid prediction for GeneMark_model.3771_t
Valid prediction for GeneMark_model.3743_t
Valid prediction for GeneMark_model.3757_t
Valid prediction for Augustus_model.g1836.t1
Valid prediction for pasa_asmbl_2548.p1
Valid prediction for snap_scaffold_1-snap.3367-T1
Valid prediction for snap_scaffold_1-snap.3369-T1
Valid prediction for GeneMark_model.3769_t
Valid prediction for Augustus_model.g1832.t1
Valid prediction for GeneMark_model.3783_t
Valid prediction for Augustus_model.g1820.t1
Valid prediction for snap_scaffold_1-snap.3399-T1
Valid prediction for GeneMark_model.3780_t
Valid prediction for GeneMark_model.3766_t
Valid prediction for GeneMark_model.3753_t
Valid prediction for GlimmerHMM_glimmerT_2549-T1
Valid prediction for GlimmerHMM_glimmerT_2532-T1
Valid prediction for snap_scaffold_1-snap.3391-T1
Valid prediction for snap_scaffold_1-snap.3378-T1
Valid prediction for GeneMark_model.3759_t
Valid prediction for GlimmerHMM_glimmerT_2533-T1
Valid prediction for GeneMark_model.3775_t
Valid prediction for GlimmerHMM_glimmerT_2535-T1
Valid prediction for snap_scaffold_1-snap.3393-T1
Valid prediction for GeneMark_model.3745_t
Valid prediction for GeneMark_model.3764_t
Valid prediction for GlimmerHMM_glimmerT_2542-T1
Valid prediction for GlimmerHMM_glimmerT_2550-T1
Valid prediction for snap_scaffold_1-snap.3398-T1
Valid prediction for GlimmerHMM_glimmerT_2539-T1
Valid prediction for GeneMark_model.3750_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.3749_t
Valid prediction for GeneMark_model.3762_t
Valid prediction for GeneMark_model.3735_t
Valid prediction for GeneMark_model.3737_t
Valid prediction for GeneMark_model.3754_t
Valid prediction for GlimmerHMM_glimmerT_2553-T1
Valid prediction for pasa_asmbl_1106.p1
Valid prediction for GeneMark_model.3746_t
Valid prediction for GeneMark_model.3774_t
Valid prediction for GeneMark_model.3752_t
Valid prediction for snap_scaffold_1-snap.3392-T1
Valid prediction for snap_scaffold_1-snap.3390-T1
Valid prediction for snap_scaffold_1-snap.3372-T1
Valid prediction for Augustus_model.g1837.t1
Valid prediction for GlimmerHMM_glimmerT_2551-T1
Valid prediction for GlimmerHMM_glimmerT_2543-T1
Valid prediction for snap_scaffold_1-snap.3382-T1
Valid prediction for GlimmerHMM_glimmerT_2540-T1
Valid prediction for GeneMark_model.3756_t
Valid prediction for Augustus_model.g1831.t1
Valid prediction for GeneMark_model.3779_t
Couldn't classify 5698, 5842
Sorry, prediction pasa_asmbl_1114.p1 fails validation.
(GGT)	 TA	5698-5842	GT	AGG
(GTC)	 AG	6057-6836	GT	GGG
(GAC)	 AG	6978-7222	CG	AAC
-recovered pasa_asmbl_1114.p1, terminal, 6978, 7222
-recovered pasa_asmbl_1114.p1, internal, 6057, 6836
Valid prediction for GlimmerHMM_glimmerT_2547-T1
Valid prediction for GeneMark_model.3758_t
Valid prediction for snap_scaffold_1-snap.3373-T1
Valid prediction for GeneMark_model.3767_t
Valid prediction for snap_scaffold_1-snap.3380-T1
Valid prediction for snap_scaffold_1-snap.3400-T1
Valid prediction for GeneMark_model.3744_t
Valid prediction for Augustus_model.g1826.t1
Valid prediction for GlimmerHMM_glimmerT_2541-T1
Valid prediction for snap_scaffold_1-snap.3387-T1
Valid prediction for snap_scaffold_1-snap.3385-T1
Valid prediction for Augustus_model.g1824.t1
Valid prediction for Augustus_model.g1838.t1
Valid prediction for GlimmerHMM_glimmerT_2548-T1
Valid prediction for snap_scaffold_1-snap.3375-T1
Valid prediction for Augustus_model.g1825.t1
Valid prediction for GeneMark_model.3772_t
Valid prediction for snap_scaffold_1-snap.3395-T1
Valid prediction for snap_scaffold_1-snap.3401-T1
Valid prediction for GlimmerHMM_glimmerT_2530-T1
Valid prediction for snap_scaffold_1-snap.3394-T1
Valid prediction for Augustus_model.g1827.t1
Valid prediction for GeneMark_model.3763_t
Valid prediction for GlimmerHMM_glimmerT_2538-T1
Valid prediction for snap_scaffold_1-snap.3384-T1
Valid prediction for GeneMark_model.3782_t
Valid prediction for GlimmerHMM_glimmerT_2536-T1
Valid prediction for GlimmerHMM_glimmerT_2552-T1
Valid prediction for CodingQuarry_transcript_2993-T1
Valid prediction for snap_scaffold_1-snap.3397-T1
Valid prediction for GeneMark_model.3781_t
Valid prediction for GeneMark_model.3776_t
Valid prediction for snap_scaffold_1-snap.3377-T1
Valid prediction for GlimmerHMM_glimmerT_2531-T1
Valid prediction for Augustus_model.g1828.t1
Valid prediction for GlimmerHMM_glimmerT_2534-T1
Valid prediction for snap_scaffold_1-snap.3388-T1
Valid prediction for GeneMark_model.3760_t
Valid prediction for GeneMark_model.3768_t
Valid prediction for GeneMark_model.3770_t
Valid prediction for snap_scaffold_1-snap.3381-T1
Valid prediction for GeneMark_model.3784_t
Valid prediction for Augustus_model.g1840.t1
Valid prediction for Augustus_model.g1821.t1
Valid prediction for HiQ_model.g1833.t1
Valid prediction for Augustus_model.g1834.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 36683, rend_intergenic: 36680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36898, rend_intergenic: 34249  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44203, rend_intergenic: 43377  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50834, rend_intergenic: 45048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55048, rend_intergenic: 52562  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57792, rend_intergenic: 55100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85908, rend_intergenic: 81095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111508, rend_intergenic: 109260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112954, rend_intergenic: 111955  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115484, rend_intergenic: 113100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125481, rend_intergenic: 120646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149126, rend_intergenic: 144313  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 168821
-exon list size: 535


building trellis

0.2    
0.4    
0.6    
0.7    
0.9    
1.1    
1.3    
1.5    
1.7    
1.9    
2.0    
2.2    
2.4    
2.6    
2.8    
3.0    
3.2    
3.4    
3.5    
3.7    
3.9    
4.1    
4.3    
4.5    
4.7    
4.8    
5.0    
5.2    
5.4    
5.6    
5.8    
6.0    
6.1    
6.3    
6.5    
6.7    
6.9    
7.1    
7.3    
7.4    
7.6    
7.8    
8.0    
8.2    
8.4    
8.6    
8.8    
8.9    
9.1    
9.3    
9.5    
9.7    
9.9    
10.1    
10.2    
10.4    
10.6    
10.8    
11.0    
11.2    
11.4    
11.5    
11.7    
11.9    
12.1    
12.3    
12.5    
12.7    
12.8    
13.0    
13.2    
13.4    
13.6    
13.8    
14.0    
14.2    
14.3    
14.5    
14.7    
14.9    
15.1    
15.3    
15.5    
15.6    
15.8    
16.0    
16.2    
16.4    
16.6    
16.8    
16.9    
17.1    
17.3    
17.5    
17.7    
17.9    
18.1    
18.2    
18.4    
18.6    
18.8    
19.0    
19.2    
19.4    
19.6    
19.7    
19.9    
20.1    
20.3    
20.5    
20.7    
20.9    
21.0    
21.2    
21.4    
21.6    
21.8    
22.0    
22.2    
22.3    
22.5    
22.7    
22.9    
23.1    
23.3    
23.5    
23.6    
23.8    
24.0    
24.2    
24.4    
24.6    
24.8    
25.0    
25.1    
25.3    
25.5    
25.7    
25.9    
26.1    
26.3    
26.4    
26.6    
26.8    
27.0    
27.2    
27.4    
27.6    
27.7    
27.9    
28.1    
28.3    
28.5    
28.7    
28.9    
29.1    
29.2    
29.4    
29.6    
29.8    
30.0    
30.2    
30.4    
30.5    
30.7    
30.9    
31.1    
31.3    
31.5    
31.7    
31.8    
32.0    
32.2    
32.4    
32.6    
32.8    
33.0    
33.1    
33.3    
33.5    
33.7    
33.9    
34.1    
34.3    
34.5    
34.6    
34.8    
35.0    
35.2    
35.4    
35.6    
35.8    
35.9    
36.1    
36.3    
36.5    
36.7    
36.9    
37.1    
37.2    
37.4    
37.6    
37.8    
38.0    
38.2    
38.4    
38.5    
38.7    
38.9    
39.1    
39.3    
39.5    
39.7    
39.9    
40.0    
40.2    
40.4    
40.6    
40.8    
41.0    
41.2    
41.3    
41.5    
41.7    
41.9    
42.1    
42.3    
42.5    
42.6    
42.8    
43.0    
43.2    
43.4    
43.6    
43.8    
43.9    
44.1    
44.3    
44.5    
44.7    
44.9    
45.1    
45.3    
45.4    
45.6    
45.8    
46.0    
46.2    
46.4    
46.6    
46.7    
46.9    
47.1    
47.3    
47.5    
47.7    
47.9    
48.0    
48.2    
48.4    
48.6    
48.8    
49.0    
49.2    
49.3    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.7    
50.8    
51.0    
51.2    
51.4    
51.6    
51.8    
52.0    
52.1    
52.3    
52.5    
52.7    
52.9    
53.1    
53.3    
53.4    
53.6    
53.8    
54.0    
54.2    
54.4    
54.6    
54.7    
54.9    
55.1    
55.3    
55.5    
55.7    
55.9    
56.1    
56.2    
56.4    
56.6    
56.8    
57.0    
57.2    
57.4    
57.5    
57.7    
57.9    
58.1    
58.3    
58.5    
58.7    
58.8    
59.0    
59.2    
59.4    
59.6    
59.8    
60.0    
60.1    
60.3    
60.5    
60.7    
60.9    
61.1    
61.3    
61.5    
61.6    
61.8    
62.0    
62.2    
62.4    
62.6    
62.8    
62.9    
63.1    
63.3    
63.5    
63.7    
63.9    
64.1    
64.2    
64.4    
64.6    
64.8    
65.0    
65.2    
65.4    
65.5    
65.7    
65.9    
66.1    
66.3    
66.5    
66.7    
66.9    
67.0    
67.2    
67.4    
67.6    
67.8    
68.0    
68.2    
68.3    
68.5    
68.7    
68.9    
69.1    
69.3    
69.5    
69.6    
69.8    
70.0    
70.2    
70.4    
70.6    
70.8    
70.9    
71.1    
71.3    
71.5    
71.7    
71.9    
72.1    
72.3    
72.4    
72.6    
72.8    
73.0    
73.2    
73.4    
73.6    
73.7    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.5    
76.7    
76.9    
77.1    
77.3    
77.5    
77.7    
77.8    
78.0    
78.2    
78.4    
78.6    
78.8    
79.0    
79.1    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.4    
80.6    
80.8    
81.0    
81.2    
81.4    
81.6    
81.8    
81.9    
82.1    
82.3    
82.5    
82.7    
82.9    
83.1    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.4    
84.5    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
85.8    
86.0    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.4    
99.6    
99.8    
-found 37 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 36683, rend_intergenic: 36680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36898, rend_intergenic: 34249  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44203, rend_intergenic: 43377  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50834, rend_intergenic: 45048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55048, rend_intergenic: 52562  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57792, rend_intergenic: 55100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85908, rend_intergenic: 81095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111508, rend_intergenic: 109260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112954, rend_intergenic: 111955  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115484, rend_intergenic: 113100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125481, rend_intergenic: 120646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149126, rend_intergenic: 144313  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support