-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_13/scaffold_13_16400405-16527564

-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_13-snap.3232-T1
Valid prediction for snap_scaffold_13-snap.3244-T1
Valid prediction for snap_scaffold_13-snap.3247-T1
Valid prediction for GeneMark_model.58056_t
Valid prediction for Augustus_model.g22706.t1
Valid prediction for pasa_asmbl_11553.p1
Valid prediction for GeneMark_model.58048_t
Valid prediction for GlimmerHMM_glimmerT_33816-T1
Valid prediction for GeneMark_model.58068_t
Valid prediction for snap_scaffold_13-snap.3249-T1
Valid prediction for GlimmerHMM_glimmerT_33802-T1
Valid prediction for GeneMark_model.58070_t
Valid prediction for snap_scaffold_13-snap.3238-T1
Valid prediction for GeneMark_model.58053_t
Couldn't classify 126995, 127156
Sorry, prediction GlimmerHMM_glimmerT_33820-T1 fails validation.
(ATG)	 AA	126015-126761	GT	AGG
(GCT)	 AG	126995-127156	GT	GGG
-recovered GlimmerHMM_glimmerT_33820-T1, initial, 126015, 126761
-recovered GlimmerHMM_glimmerT_33820-T1, internal, 126995, 127156
Valid prediction for GlimmerHMM_glimmerT_33803-T1
Couldn't classify 126995, 127137
Sorry, prediction GeneMark_model.58071_t fails validation.
(ATG)	 TC	126027-126761	GT	AGG
(GCT)	 AG	126995-127137	GC	GGG
-recovered GeneMark_model.58071_t, initial, 126027, 126761
-recovered GeneMark_model.58071_t, internal, 126995, 127137
Valid prediction for Augustus_model.g22707.t1
Valid prediction for snap_scaffold_13-snap.3250-T1
Valid prediction for snap_scaffold_13-snap.3254-T1
Valid prediction for GeneMark_model.58054_t
Valid prediction for GlimmerHMM_glimmerT_33817-T1
Valid prediction for GlimmerHMM_glimmerT_33811-T1
Valid prediction for GeneMark_model.58058_t
Valid prediction for GeneMark_model.58046_t
Valid prediction for snap_scaffold_13-snap.3226-T1
Valid prediction for GeneMark_model.58061_t
Valid prediction for GlimmerHMM_glimmerT_33814-T1
Valid prediction for GlimmerHMM_glimmerT_33806-T1
Valid prediction for GlimmerHMM_glimmerT_33813-T1
Couldn't classify 126995, 127156
Sorry, prediction snap_scaffold_13-snap.3255-T1 fails validation.
(ATG)	 TC	126027-126761	GT	AGG
(GCT)	 AG	126995-127156	GT	GGG
-recovered snap_scaffold_13-snap.3255-T1, initial, 126027, 126761
-recovered snap_scaffold_13-snap.3255-T1, internal, 126995, 127156
Couldn't classify 118371, 118565
Sorry, prediction pasa_asmbl_11561.p1 fails validation.
(GTG)	 GG	118371-118565	GT	GAG
(CCT)	 AG	118670-118878	GT	CTG
(GAT)	 AG	119632-119800	GT	GGG
(GAG)	 AG	120106-120156	GT	ATG
(GAT)	 AG	120836-120940	AG	GAA
-recovered pasa_asmbl_11561.p1, terminal, 120836, 120940
-recovered pasa_asmbl_11561.p1, internal, 118670, 118878
-recovered pasa_asmbl_11561.p1, internal, 119632, 119800
-recovered pasa_asmbl_11561.p1, internal, 120106, 120156
Valid prediction for Augustus_model.g22708.t1
Valid prediction for GeneMark_model.58043_t
Valid prediction for Augustus_model.g22705.t1
Valid prediction for GeneMark_model.58066_t
Valid prediction for GeneMark_model.58064_t
Valid prediction for snap_scaffold_13-snap.3242-T1
Valid prediction for snap_scaffold_13-snap.3234-T1
Valid prediction for CodingQuarry_transcript_13329-T1
Valid prediction for GeneMark_model.58065_t
Valid prediction for GlimmerHMM_glimmerT_33808-T1
Valid prediction for GeneMark_model.58049_t
Valid prediction for HiQ_model.g22699.t1
Valid prediction for snap_scaffold_13-snap.3233-T1
Valid prediction for snap_scaffold_13-snap.3252-T1
Valid prediction for snap_scaffold_13-snap.3229-T1
Valid prediction for pasa_asmbl_11550.p1
Valid prediction for GlimmerHMM_glimmerT_33805-T1
Valid prediction for HiQ_model.g22702.t1
Valid prediction for snap_scaffold_13-snap.3239-T1
Valid prediction for snap_scaffold_13-snap.3227-T1
Valid prediction for snap_scaffold_13-snap.3225-T1
Valid prediction for GeneMark_model.58063_t
Valid prediction for Augustus_model.g22698.t1
Valid prediction for GlimmerHMM_glimmerT_33818-T1
Valid prediction for GlimmerHMM_glimmerT_33801-T1
Valid prediction for GlimmerHMM_glimmerT_33807-T1
Valid prediction for snap_scaffold_13-snap.3245-T1
Valid prediction for snap_scaffold_13-snap.3236-T1
Valid prediction for snap_scaffold_13-snap.3231-T1
Valid prediction for GeneMark_model.58051_t
Valid prediction for GeneMark_model.58069_t
Valid prediction for HiQ_model.g22700.t1
Valid prediction for pasa_asmbl_11551.p1
Valid prediction for GlimmerHMM_glimmerT_33819-T1
Valid prediction for GeneMark_model.58044_t
Valid prediction for CodingQuarry_transcript_13328-T1
Valid prediction for CodingQuarry_transcript_13330-T1
Valid prediction for snap_scaffold_13-snap.3224-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 GeneMark_model.58062_t
Valid prediction for snap_scaffold_13-snap.3251-T1
Valid prediction for GeneMark_model.58050_t
Valid prediction for GeneMark_model.58045_t
Valid prediction for snap_scaffold_13-snap.3228-T1
Valid prediction for GlimmerHMM_glimmerT_33804-T1
Valid prediction for snap_scaffold_13-snap.3235-T1
Valid prediction for CodingQuarry_transcript_13331-T1
Valid prediction for snap_scaffold_13-snap.3223-T1
Valid prediction for GlimmerHMM_glimmerT_33812-T1
Valid prediction for snap_scaffold_13-snap.3246-T1
Valid prediction for GlimmerHMM_glimmerT_33800-T1
Valid prediction for snap_scaffold_13-snap.3253-T1
Valid prediction for GeneMark_model.58057_t
Valid prediction for GeneMark_model.58047_t
Valid prediction for snap_scaffold_13-snap.3243-T1
Valid prediction for GeneMark_model.58059_t
Valid prediction for pasa_asmbl_10301.p1
Valid prediction for Augustus_model.g22701.t1
Valid prediction for GlimmerHMM_glimmerT_33809-T1
Valid prediction for GlimmerHMM_glimmerT_33815-T1
Valid prediction for HiQ_model.g22704.t1
Valid prediction for snap_scaffold_13-snap.3241-T1
Valid prediction for snap_scaffold_13-snap.3237-T1
Valid prediction for snap_scaffold_13-snap.3240-T1
Valid prediction for GlimmerHMM_glimmerT_33810-T1
Valid prediction for snap_scaffold_13-snap.3230-T1
Valid prediction for GeneMark_model.58067_t
Valid prediction for snap_scaffold_13-snap.3248-T1
Valid prediction for GeneMark_model.58052_t
Valid prediction for HiQ_model.g22703.t1
Valid prediction for GeneMark_model.58055_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14724, rend_intergenic: 3719  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26158, rend_intergenic: 24751  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33362, rend_intergenic: 30739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50089, rend_intergenic: 41656  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56634, rend_intergenic: 52326  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74199, rend_intergenic: 67576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77611, rend_intergenic: 74367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79693, rend_intergenic: 79028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97671, rend_intergenic: 81117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103402, rend_intergenic: 100645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106406, rend_intergenic: 103724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115605, rend_intergenic: 111884  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118015, rend_intergenic: 117462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120940, rend_intergenic: 118325  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 127160
-exon list size: 406


building trellis

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1.0    
1.2    
1.5    
1.7    
2.0    
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2.5    
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2.9    
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3.4    
3.7    
3.9    
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4.9    
5.1    
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5.9    
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8.8    
9.1    
9.3    
9.6    
9.8    
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10.3    
10.5    
10.8    
11.0    
11.3    
11.5    
11.8    
12.0    
12.3    
12.5    
12.7    
13.0    
13.2    
13.5    
13.7    
14.0    
14.2    
14.5    
14.7    
15.0    
15.2    
15.4    
15.7    
15.9    
16.2    
16.4    
16.7    
16.9    
17.2    
17.4    
17.6    
17.9    
18.1    
18.4    
18.6    
18.9    
19.1    
19.4    
19.6    
19.9    
20.1    
20.3    
20.6    
20.8    
21.1    
21.3    
21.6    
21.8    
22.1    
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    
27.9    
28.2    
28.4    
28.7    
28.9    
29.2    
29.4    
29.7    
29.9    
30.1    
30.4    
30.6    
30.9    
31.1    
31.4    
31.6    
31.9    
32.1    
32.4    
32.6    
32.8    
33.1    
33.3    
33.6    
33.8    
34.1    
34.3    
34.6    
34.8    
35.0    
35.3    
35.5    
35.8    
36.0    
36.3    
36.5    
36.8    
37.0    
37.3    
37.5    
37.7    
38.0    
38.2    
38.5    
38.7    
39.0    
39.2    
39.5    
39.7    
40.0    
40.2    
40.4    
40.7    
40.9    
41.2    
41.4    
41.7    
41.9    
42.2    
42.4    
42.6    
42.9    
43.1    
43.4    
43.6    
43.9    
44.1    
44.4    
44.6    
44.9    
45.1    
45.3    
45.6    
45.8    
46.1    
46.3    
46.6    
46.8    
47.1    
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    
52.9    
53.2    
53.4    
53.7    
53.9    
54.2    
54.4    
54.7    
54.9    
55.1    
55.4    
55.6    
55.9    
56.1    
56.4    
56.6    
56.9    
57.1    
57.4    
57.6    
57.8    
58.1    
58.3    
58.6    
58.8    
59.1    
59.3    
59.6    
59.8    
60.0    
60.3    
60.5    
60.8    
61.0    
61.3    
61.5    
61.8    
62.0    
62.3    
62.5    
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63.2    
63.5    
63.7    
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64.5    
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65.0    
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65.4    
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65.9    
66.2    
66.4    
66.7    
66.9    
67.2    
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67.6    
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68.1    
68.4    
68.6    
68.9    
69.1    
69.4    
69.6    
69.9    
70.1    
70.3    
70.6    
70.8    
71.1    
71.3    
71.6    
71.8    
72.1    
72.3    
72.5    
72.8    
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    
77.9    
78.2    
78.4    
78.7    
78.9    
79.2    
79.4    
79.7    
79.9    
80.1    
80.4    
80.6    
80.9    
81.1    
81.4    
81.6    
81.9    
82.1    
82.4    
82.6    
82.8    
83.1    
83.3    
83.6    
83.8    
84.1    
84.3    
84.6    
84.8    
85.0    
85.3    
85.5    
85.8    
86.0    
86.3    
86.5    
86.8    
87.0    
87.3    
87.5    
87.7    
88.0    
88.2    
88.5    
88.7    
89.0    
89.2    
89.5    
89.7    
90.0    
90.2    
90.4    
90.7    
90.9    
91.2    
91.4    
91.7    
91.9    
92.2    
92.4    
92.6    
92.9    
93.1    
93.4    
93.6    
93.9    
94.1    
94.4    
94.6    
94.9    
95.1    
95.3    
95.6    
95.8    
96.1    
96.3    
96.6    
96.8    
97.1    
97.3    
97.5    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 14724, rend_intergenic: 3719  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26158, rend_intergenic: 24751  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33362, rend_intergenic: 30739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50089, rend_intergenic: 41656  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56634, rend_intergenic: 52326  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74199, rend_intergenic: 67576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77611, rend_intergenic: 74367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79693, rend_intergenic: 79028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97671, rend_intergenic: 81117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103402, rend_intergenic: 100645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106406, rend_intergenic: 103724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115605, rend_intergenic: 111884  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118015, rend_intergenic: 117462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120940, rend_intergenic: 118325  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support