-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_11/scaffold_11_13963543-14169045

-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 Augustus_model.g19245.t1
Valid prediction for snap_scaffold_11-snap.2968-T1
Valid prediction for snap_scaffold_11-snap.2965-T1
Valid prediction for GeneMark_model.49783_t
Valid prediction for snap_scaffold_11-snap.2986-T1
Valid prediction for GeneMark_model.49797_t
Valid prediction for Augustus_model.g19252.t1
Valid prediction for GlimmerHMM_glimmerT_28826-T1
Valid prediction for Augustus_model.g19244.t1
Valid prediction for GeneMark_model.49770_t
Valid prediction for snap_scaffold_11-snap.2960-T1
Valid prediction for GeneMark_model.49802_t
Valid prediction for snap_scaffold_11-snap.2969-T1
Valid prediction for GlimmerHMM_glimmerT_28831-T1
Valid prediction for GeneMark_model.49801_t
Valid prediction for GlimmerHMM_glimmerT_28841-T1
Valid prediction for snap_scaffold_11-snap.2967-T1
Valid prediction for GlimmerHMM_glimmerT_28835-T1
Valid prediction for GeneMark_model.49775_t
Valid prediction for GeneMark_model.49786_t
Valid prediction for snap_scaffold_11-snap.2972-T1
Valid prediction for GlimmerHMM_glimmerT_28839-T1
Valid prediction for GlimmerHMM_glimmerT_28828-T1
Valid prediction for snap_scaffold_11-snap.2979-T1
Valid prediction for snap_scaffold_11-snap.2988-T1
Valid prediction for GeneMark_model.49764_t
Valid prediction for GlimmerHMM_glimmerT_28820-T1
Valid prediction for GlimmerHMM_glimmerT_28840-T1
Valid prediction for GlimmerHMM_glimmerT_28834-T1
Valid prediction for snap_scaffold_11-snap.2973-T1
Valid prediction for snap_scaffold_11-snap.2962-T1
Valid prediction for GeneMark_model.49789_t
Valid prediction for Augustus_model.g19251.t1
Valid prediction for snap_scaffold_11-snap.2981-T1
Valid prediction for Augustus_model.g19253.t1
Valid prediction for Augustus_model.g19246.t1
Valid prediction for GeneMark_model.49799_t
Valid prediction for GeneMark_model.49805_t
Valid prediction for GeneMark_model.49792_t
Valid prediction for GeneMark_model.49791_t
Valid prediction for GeneMark_model.49772_t
Valid prediction for snap_scaffold_11-snap.2978-T1
Valid prediction for GlimmerHMM_glimmerT_28833-T1
Valid prediction for snap_scaffold_11-snap.2971-T1
Valid prediction for GeneMark_model.49779_t
Valid prediction for Augustus_model.g19250.t1
Valid prediction for GeneMark_model.49767_t
Valid prediction for Augustus_model.g19248.t1
Valid prediction for GeneMark_model.49795_t
Valid prediction for GeneMark_model.49765_t
Valid prediction for GeneMark_model.49776_t
Valid prediction for snap_scaffold_11-snap.2983-T1
Valid prediction for GeneMark_model.49793_t
Valid prediction for snap_scaffold_11-snap.2963-T1
Valid prediction for GlimmerHMM_glimmerT_28836-T1
Valid prediction for GeneMark_model.49782_t
Valid prediction for snap_scaffold_11-snap.2970-T1
Valid prediction for snap_scaffold_11-snap.2984-T1
Valid prediction for GlimmerHMM_glimmerT_28829-T1
Valid prediction for GeneMark_model.49773_t
Valid prediction for GlimmerHMM_glimmerT_28823-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_11-snap.2985-T1
Valid prediction for GlimmerHMM_glimmerT_28842-T1
Couldn't classify 40245, 40298
Sorry, prediction pasa_asmbl_7135.p1 fails validation.
(TTT)	 AG	40245-40298	GT	AGG
(ATG)	 AG	40931-41090	GT	GGG
(CTG)	 AG	41231-41286	GT	TGG
(GAA)	 AG	41473-41542	GT	GAG
(TTC)	 AG	42349-42436	GT	CGG
(GTA)	 AG	42687-42795	GT	TTG
(CTG)	 AG	42994-43086	GT	AGG
(GTT)	 AG	44180-44312	GT	GTG
(CTC)	 AG	44450-44570	GT	AAG
(ATG)	 AG	45121-45179	GT	AGG
(ATG)	 AG	46595-46770	GT	AGG
(AAG)	 AG	49558-49648	GT	AGG
(AGG)	 AG	49825-50033	TC	AGT
-recovered pasa_asmbl_7135.p1, initial, 40931, 41090
add_exon() Sorry, pasa_asmbl_7135.p1 45121-45179-initial-1 is invalid.
-recovered pasa_asmbl_7135.p1, initial, 45121, 45179
add_exon() Sorry, pasa_asmbl_7135.p1 46595-46770-initial-1 is invalid.
-recovered pasa_asmbl_7135.p1, initial, 46595, 46770
-recovered pasa_asmbl_7135.p1, terminal, 41473, 41542
-recovered pasa_asmbl_7135.p1, terminal, 49825, 50033
-recovered pasa_asmbl_7135.p1, internal, 40245, 40298
-recovered pasa_asmbl_7135.p1, internal, 40931, 41090
-recovered pasa_asmbl_7135.p1, internal, 41231, 41286
-recovered pasa_asmbl_7135.p1, internal, 41473, 41542
-recovered pasa_asmbl_7135.p1, internal, 42349, 42436
-recovered pasa_asmbl_7135.p1, internal, 42687, 42795
-recovered pasa_asmbl_7135.p1, internal, 42994, 43086
-recovered pasa_asmbl_7135.p1, internal, 44180, 44312
-recovered pasa_asmbl_7135.p1, internal, 44450, 44570
-recovered pasa_asmbl_7135.p1, internal, 45121, 45179
-recovered pasa_asmbl_7135.p1, internal, 46595, 46770
-recovered pasa_asmbl_7135.p1, internal, 49558, 49648
Valid prediction for snap_scaffold_11-snap.2989-T1
Valid prediction for GlimmerHMM_glimmerT_28822-T1
Valid prediction for GeneMark_model.49778_t
Valid prediction for snap_scaffold_11-snap.2987-T1
Valid prediction for GeneMark_model.49790_t
Valid prediction for GlimmerHMM_glimmerT_28830-T1
Valid prediction for HiQ_model.g19249.t1
Valid prediction for snap_scaffold_11-snap.2974-T1
Valid prediction for snap_scaffold_11-snap.2966-T1
Valid prediction for GeneMark_model.49777_t
Valid prediction for GlimmerHMM_glimmerT_28821-T1
Valid prediction for GeneMark_model.49787_t
Valid prediction for snap_scaffold_11-snap.2959-T1
Valid prediction for GlimmerHMM_glimmerT_28827-T1
Valid prediction for GeneMark_model.49798_t
Valid prediction for snap_scaffold_11-snap.2976-T1
Valid prediction for GlimmerHMM_glimmerT_28838-T1
Valid prediction for GeneMark_model.49769_t
Valid prediction for Augustus_model.g19247.t1
Valid prediction for GeneMark_model.49788_t
Valid prediction for GeneMark_model.49768_t
Valid prediction for GeneMark_model.49785_t
Valid prediction for GeneMark_model.49771_t
Valid prediction for GeneMark_model.49781_t
Valid prediction for GlimmerHMM_glimmerT_28837-T1
Valid prediction for GeneMark_model.49774_t
Valid prediction for GeneMark_model.49796_t
Valid prediction for GeneMark_model.49766_t
Valid prediction for GlimmerHMM_glimmerT_28825-T1
Valid prediction for snap_scaffold_11-snap.2977-T1
Valid prediction for snap_scaffold_11-snap.2961-T1
Valid prediction for GeneMark_model.49803_t
Valid prediction for GeneMark_model.49806_t
Valid prediction for GeneMark_model.49800_t
Valid prediction for GlimmerHMM_glimmerT_28832-T1
Valid prediction for snap_scaffold_11-snap.2980-T1
Valid prediction for snap_scaffold_11-snap.2982-T1
Valid prediction for GeneMark_model.49804_t
Valid prediction for GlimmerHMM_glimmerT_28824-T1
Valid prediction for snap_scaffold_11-snap.2975-T1
Valid prediction for snap_scaffold_11-snap.2964-T1
Valid prediction for GeneMark_model.49780_t
Valid prediction for GeneMark_model.49794_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6227, rend_intergenic: 4240  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7936, rend_intergenic: 6649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34126, rend_intergenic: 28181  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54309, rend_intergenic: 38252  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156176, rend_intergenic: 139630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177845, rend_intergenic: 175126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199356, rend_intergenic: 196651  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203198, rend_intergenic: 199620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 205503
-exon list size: 474


building trellis

0.2    
0.4    
0.6    
0.8    
1.1    
1.3    
1.5    
1.7    
1.9    
2.1    
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2.5    
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2.9    
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3.4    
3.6    
3.8    
4.0    
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5.9    
6.1    
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6.9    
7.1    
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7.6    
7.8    
8.0    
8.2    
8.4    
8.6    
8.8    
9.0    
9.2    
9.5    
9.7    
9.9    
10.1    
10.3    
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10.9    
11.1    
11.3    
11.6    
11.8    
12.0    
12.2    
12.4    
12.6    
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13.2    
13.4    
13.7    
13.9    
14.1    
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14.9    
15.1    
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15.5    
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16.0    
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16.6    
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17.6    
17.9    
18.1    
18.3    
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18.7    
18.9    
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19.3    
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19.7    
20.0    
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20.6    
20.8    
21.0    
21.2    
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21.8    
22.1    
22.3    
22.5    
22.7    
22.9    
23.1    
23.3    
23.5    
23.7    
23.9    
24.2    
24.4    
24.6    
24.8    
25.0    
25.2    
25.4    
25.6    
25.8    
26.1    
26.3    
26.5    
26.7    
26.9    
27.1    
27.3    
27.5    
27.7    
27.9    
28.2    
28.4    
28.6    
28.8    
29.0    
29.2    
29.4    
29.6    
29.8    
30.0    
30.3    
30.5    
30.7    
30.9    
31.1    
31.3    
31.5    
31.7    
31.9    
32.1    
32.4    
32.6    
32.8    
33.0    
33.2    
33.4    
33.6    
33.8    
34.0    
34.2    
34.5    
34.7    
34.9    
35.1    
35.3    
35.5    
35.7    
35.9    
36.1    
36.3    
36.6    
36.8    
37.0    
37.2    
37.4    
37.6    
37.8    
38.0    
38.2    
38.4    
38.7    
38.9    
39.1    
39.3    
39.5    
39.7    
39.9    
40.1    
40.3    
40.5    
40.8    
41.0    
41.2    
41.4    
41.6    
41.8    
42.0    
42.2    
42.4    
42.6    
42.9    
43.1    
43.3    
43.5    
43.7    
43.9    
44.1    
44.3    
44.5    
44.7    
45.0    
45.2    
45.4    
45.6    
45.8    
46.0    
46.2    
46.4    
46.6    
46.8    
47.1    
47.3    
47.5    
47.7    
47.9    
48.1    
48.3    
48.5    
48.7    
48.9    
49.2    
49.4    
49.6    
49.8    
50.0    
50.2    
50.4    
50.6    
50.8    
51.1    
51.3    
51.5    
51.7    
51.9    
52.1    
52.3    
52.5    
52.7    
52.9    
53.2    
53.4    
53.6    
53.8    
54.0    
54.2    
54.4    
54.6    
54.8    
55.0    
55.3    
55.5    
55.7    
55.9    
56.1    
56.3    
56.5    
56.7    
56.9    
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57.6    
57.8    
58.0    
58.2    
58.4    
58.6    
58.8    
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59.2    
59.5    
59.7    
59.9    
60.1    
60.3    
60.5    
60.7    
60.9    
61.1    
61.3    
61.6    
61.8    
62.0    
62.2    
62.4    
62.6    
62.8    
63.0    
63.2    
63.4    
63.7    
63.9    
64.1    
64.3    
64.5    
64.7    
64.9    
65.1    
65.3    
65.5    
65.8    
66.0    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
67.4    
67.6    
67.9    
68.1    
68.3    
68.5    
68.7    
68.9    
69.1    
69.3    
69.5    
69.7    
70.0    
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70.4    
70.6    
70.8    
71.0    
71.2    
71.4    
71.6    
71.8    
72.1    
72.3    
72.5    
72.7    
72.9    
73.1    
73.3    
73.5    
73.7    
73.9    
74.2    
74.4    
74.6    
74.8    
75.0    
75.2    
75.4    
75.6    
75.8    
76.1    
76.3    
76.5    
76.7    
76.9    
77.1    
77.3    
77.5    
77.7    
77.9    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.4    
79.6    
79.8    
80.0    
80.3    
80.5    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
82.1    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.5    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.3    
86.6    
86.8    
87.0    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.4    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.2    
99.4    
99.6    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 6227, rend_intergenic: 4240  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7936, rend_intergenic: 6649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34126, rend_intergenic: 28181  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54309, rend_intergenic: 38252  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156176, rend_intergenic: 139630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177845, rend_intergenic: 175126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199356, rend_intergenic: 196651  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203198, rend_intergenic: 199620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 9 predictions persist after filtering for low support