-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_19814156-20022935

-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 CodingQuarry_transcript_3018-T1
Valid prediction for GlimmerHMM_glimmerT_2656-T1
Valid prediction for snap_scaffold_1-snap.3664-T1
Valid prediction for snap_scaffold_1-snap.3663-T1
Valid prediction for snap_scaffold_1-snap.3695-T1
Valid prediction for pasa_asmbl_2603.p1
Valid prediction for snap_scaffold_1-snap.3657-T1
Valid prediction for snap_scaffold_1-snap.3671-T1
Valid prediction for GlimmerHMM_glimmerT_2679-T1
Valid prediction for snap_scaffold_1-snap.3688-T1
Valid prediction for snap_scaffold_1-snap.3673-T1
Valid prediction for snap_scaffold_1-snap.3684-T1
Valid prediction for pasa_asmbl_2599.p1
Valid prediction for Augustus_model.g1915.t1
Valid prediction for snap_scaffold_1-snap.3683-T1
Valid prediction for GlimmerHMM_glimmerT_2682-T1
Valid prediction for snap_scaffold_1-snap.3658-T1
Valid prediction for GlimmerHMM_glimmerT_2659-T1
Valid prediction for snap_scaffold_1-snap.3685-T1
Valid prediction for snap_scaffold_1-snap.3679-T1
Valid prediction for Augustus_model.g1911.t1
Valid prediction for GlimmerHMM_glimmerT_2675-T1
Valid prediction for GlimmerHMM_glimmerT_2671-T1
Valid prediction for HiQ_model.g1909.t1
Valid prediction for Augustus_model.g1916.t1
Valid prediction for snap_scaffold_1-snap.3693-T1
Valid prediction for GlimmerHMM_glimmerT_2678-T1
Valid prediction for GlimmerHMM_glimmerT_2668-T1
Valid prediction for snap_scaffold_1-snap.3670-T1
Valid prediction for GlimmerHMM_glimmerT_2681-T1
Valid prediction for GlimmerHMM_glimmerT_2669-T1
Valid prediction for snap_scaffold_1-snap.3669-T1
Valid prediction for snap_scaffold_1-snap.3662-T1
Valid prediction for GlimmerHMM_glimmerT_2666-T1
Valid prediction for snap_scaffold_1-snap.3651-T1
Valid prediction for snap_scaffold_1-snap.3691-T1
Valid prediction for snap_scaffold_1-snap.3678-T1
Valid prediction for snap_scaffold_1-snap.3660-T1
Valid prediction for snap_scaffold_1-snap.3667-T1
Valid prediction for snap_scaffold_1-snap.3696-T1
Valid prediction for snap_scaffold_1-snap.3666-T1
Valid prediction for snap_scaffold_1-snap.3681-T1
Valid prediction for snap_scaffold_1-snap.3675-T1
Valid prediction for snap_scaffold_1-snap.3654-T1
Valid prediction for CodingQuarry_transcript_3019-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 snap_scaffold_1-snap.3661-T1
Valid prediction for GlimmerHMM_glimmerT_2663-T1
Valid prediction for GlimmerHMM_glimmerT_2680-T1
Valid prediction for snap_scaffold_1-snap.3655-T1
Valid prediction for GlimmerHMM_glimmerT_2657-T1
Valid prediction for GlimmerHMM_glimmerT_2670-T1
Valid prediction for GlimmerHMM_glimmerT_2677-T1
Valid prediction for GlimmerHMM_glimmerT_2665-T1
Valid prediction for GlimmerHMM_glimmerT_2672-T1
Valid prediction for GlimmerHMM_glimmerT_2662-T1
Valid prediction for GlimmerHMM_glimmerT_2676-T1
Valid prediction for snap_scaffold_1-snap.3652-T1
Valid prediction for snap_scaffold_1-snap.3674-T1
Valid prediction for snap_scaffold_1-snap.3656-T1
Valid prediction for snap_scaffold_1-snap.3686-T1
Valid prediction for GlimmerHMM_glimmerT_2661-T1
Valid prediction for snap_scaffold_1-snap.3672-T1
Valid prediction for GlimmerHMM_glimmerT_2674-T1
Valid prediction for snap_scaffold_1-snap.3689-T1
Valid prediction for snap_scaffold_1-snap.3680-T1
Couldn't classify 198306, 198450
Couldn't classify 199515, 199618
Sorry, prediction pasa_asmbl_1157.p1 fails validation.
(GAG)	 GC	198306-198450	GT	TGG
(ATG)	 AG	199062-199235	GT	CGG
(GTG)	 AG	199515-199618	GG	GAG
add_exon() Sorry, pasa_asmbl_1157.p1 199062-199235-initial-1 is invalid.
-recovered pasa_asmbl_1157.p1, initial, 199062, 199235
-recovered pasa_asmbl_1157.p1, internal, 199062, 199235
Valid prediction for Augustus_model.g1910.t1
Valid prediction for snap_scaffold_1-snap.3682-T1
Valid prediction for snap_scaffold_1-snap.3692-T1
Valid prediction for Augustus_model.g1914.t1
Valid prediction for snap_scaffold_1-snap.3694-T1
Valid prediction for snap_scaffold_1-snap.3668-T1
Valid prediction for snap_scaffold_1-snap.3676-T1
Valid prediction for GlimmerHMM_glimmerT_2660-T1
Valid prediction for snap_scaffold_1-snap.3677-T1
Valid prediction for snap_scaffold_1-snap.3690-T1
Valid prediction for Augustus_model.g1913.t1
Valid prediction for GlimmerHMM_glimmerT_2667-T1
Couldn't classify 78319, 78479
Sorry, prediction pasa_asmbl_1159.p1 fails validation.
(ACC)	 AG	78319-78479	GT	AGG
(GAA)	 AG	78803-79043	GT	AGG
(GTG)	 AG	79320-79482	GT	CGG
(CTC)	 AG	80296-80483	GT	CTG
(GTG)	 AG	80965-81069	GT	CTG
(CTG)	 AG	81353-81454	GT	TGG
(GAA)	 AG	82006-82209	GT	TGG
(GAT)	 AG	82434-82631	GC	GAG
-recovered pasa_asmbl_1159.p1, terminal, 82434, 82631
-recovered pasa_asmbl_1159.p1, internal, 78319, 78479
-recovered pasa_asmbl_1159.p1, internal, 78803, 79043
-recovered pasa_asmbl_1159.p1, internal, 79320, 79482
-recovered pasa_asmbl_1159.p1, internal, 80296, 80483
-recovered pasa_asmbl_1159.p1, internal, 80965, 81069
-recovered pasa_asmbl_1159.p1, internal, 81353, 81454
-recovered pasa_asmbl_1159.p1, internal, 82006, 82209
-recovered pasa_asmbl_1159.p1, internal, 82434, 82631
Valid prediction for GlimmerHMM_glimmerT_2673-T1
Valid prediction for GlimmerHMM_glimmerT_2664-T1
Valid prediction for snap_scaffold_1-snap.3665-T1
Valid prediction for Augustus_model.g1912.t1
Valid prediction for snap_scaffold_1-snap.3697-T1
Valid prediction for snap_scaffold_1-snap.3653-T1
Valid prediction for Augustus_model.g1908.t1
Valid prediction for snap_scaffold_1-snap.3659-T1
Valid prediction for snap_scaffold_1-snap.3687-T1
Valid prediction for GlimmerHMM_glimmerT_2658-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15328, rend_intergenic: 7394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22682, rend_intergenic: 22039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31678, rend_intergenic: 24058  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37652, rend_intergenic: 33269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40020, rend_intergenic: 37779  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56313, rend_intergenic: 41243  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68574, rend_intergenic: 58313  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89915, rend_intergenic: 68993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91729, rend_intergenic: 89994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105471, rend_intergenic: 91780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107818, rend_intergenic: 106566  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108528, rend_intergenic: 108078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114483, rend_intergenic: 108750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141780, rend_intergenic: 126238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151153, rend_intergenic: 145373  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159196, rend_intergenic: 153877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160840, rend_intergenic: 159380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163375, rend_intergenic: 161490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182619, rend_intergenic: 168170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185834, rend_intergenic: 182673  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192046, rend_intergenic: 186942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194576, rend_intergenic: 192052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202180, rend_intergenic: 196292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207581, rend_intergenic: 203499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 208780
-exon list size: 402


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
1.5    
1.7    
2.0    
2.2    
2.5    
2.7    
3.0    
3.2    
3.5    
3.7    
4.0    
4.2    
4.5    
4.7    
5.0    
5.2    
5.4    
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5.9    
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6.4    
6.7    
6.9    
7.2    
7.4    
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7.9    
8.2    
8.4    
8.7    
8.9    
9.2    
9.4    
9.7    
9.9    
10.1    
10.4    
10.6    
10.9    
11.1    
11.4    
11.6    
11.9    
12.1    
12.4    
12.6    
12.9    
13.1    
13.4    
13.6    
13.9    
14.1    
14.4    
14.6    
14.9    
15.1    
15.3    
15.6    
15.8    
16.1    
16.3    
16.6    
16.8    
17.1    
17.3    
17.6    
17.8    
18.1    
18.3    
18.6    
18.8    
19.1    
19.3    
19.6    
19.8    
20.0    
20.3    
20.5    
20.8    
21.0    
21.3    
21.5    
21.8    
22.0    
22.3    
22.5    
22.8    
23.0    
23.3    
23.5    
23.8    
24.0    
24.3    
24.5    
24.8    
25.0    
25.2    
25.5    
25.7    
26.0    
26.2    
26.5    
26.7    
27.0    
27.2    
27.5    
27.7    
28.0    
28.2    
28.5    
28.7    
29.0    
29.2    
29.5    
29.7    
30.0    
30.2    
30.4    
30.7    
30.9    
31.2    
31.4    
31.7    
31.9    
32.2    
32.4    
32.7    
32.9    
33.2    
33.4    
33.7    
33.9    
34.2    
34.4    
34.7    
34.9    
35.1    
35.4    
35.6    
35.9    
36.1    
36.4    
36.6    
36.9    
37.1    
37.4    
37.6    
37.9    
38.1    
38.4    
38.6    
38.9    
39.1    
39.4    
39.6    
39.9    
40.1    
40.3    
40.6    
40.8    
41.1    
41.3    
41.6    
41.8    
42.1    
42.3    
42.6    
42.8    
43.1    
43.3    
43.6    
43.8    
44.1    
44.3    
44.6    
44.8    
45.0    
45.3    
45.5    
45.8    
46.0    
46.3    
46.5    
46.8    
47.0    
47.3    
47.5    
47.8    
48.0    
48.3    
48.5    
48.8    
49.0    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
51.0    
51.2    
51.5    
51.7    
52.0    
52.2    
52.5    
52.7    
53.0    
53.2    
53.5    
53.7    
54.0    
54.2    
54.5    
54.7    
55.0    
55.2    
55.4    
55.7    
55.9    
56.2    
56.4    
56.7    
56.9    
57.2    
57.4    
57.7    
57.9    
58.2    
58.4    
58.7    
58.9    
59.2    
59.4    
59.7    
59.9    
60.1    
60.4    
60.6    
60.9    
61.1    
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61.6    
61.9    
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62.6    
62.9    
63.1    
63.4    
63.6    
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64.1    
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65.6    
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66.3    
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67.6    
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68.1    
68.3    
68.6    
68.8    
69.1    
69.3    
69.6    
69.8    
70.0    
70.3    
70.5    
70.8    
71.0    
71.3    
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72.0    
72.3    
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73.0    
73.3    
73.5    
73.8    
74.0    
74.3    
74.5    
74.8    
75.0    
75.2    
75.5    
75.7    
76.0    
76.2    
76.5    
76.7    
77.0    
77.2    
77.5    
77.7    
78.0    
78.2    
78.5    
78.7    
79.0    
79.2    
79.5    
79.7    
80.0    
80.2    
80.4    
80.7    
80.9    
81.2    
81.4    
81.7    
81.9    
82.2    
82.4    
82.7    
82.9    
83.2    
83.4    
83.7    
83.9    
84.2    
84.4    
84.7    
84.9    
85.1    
85.4    
85.6    
85.9    
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86.6    
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87.4    
87.6    
87.9    
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88.4    
88.6    
88.9    
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89.4    
89.6    
89.9    
90.1    
90.3    
90.6    
90.8    
91.1    
91.3    
91.6    
91.8    
92.1    
92.3    
92.6    
92.8    
93.1    
93.3    
93.6    
93.8    
94.1    
94.3    
94.6    
94.8    
95.0    
95.3    
95.5    
95.8    
96.0    
96.3    
96.5    
96.8    
97.0    
97.3    
97.5    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 15328, rend_intergenic: 7394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22682, rend_intergenic: 22039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31678, rend_intergenic: 24058  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37652, rend_intergenic: 33269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40020, rend_intergenic: 37779  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56313, rend_intergenic: 41243  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68574, rend_intergenic: 58313  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89915, rend_intergenic: 68993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91729, rend_intergenic: 89994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105471, rend_intergenic: 91780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107818, rend_intergenic: 106566  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108528, rend_intergenic: 108078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114483, rend_intergenic: 108750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141780, rend_intergenic: 126238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151153, rend_intergenic: 145373  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159196, rend_intergenic: 153877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160840, rend_intergenic: 159380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163375, rend_intergenic: 161490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182619, rend_intergenic: 168170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185834, rend_intergenic: 182673  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192046, rend_intergenic: 186942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194576, rend_intergenic: 192052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202180, rend_intergenic: 196292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207581, rend_intergenic: 203499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support