-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_17756201-17928014

-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_5-snap.3337-T1
Valid prediction for GlimmerHMM_glimmerT_13883-T1
Valid prediction for GeneMark_model.23281_t
Valid prediction for GeneMark_model.23295_t
Valid prediction for GeneMark_model.23297_t
Couldn't classify 59525, 59947
Sorry, prediction pasa_asmbl_44851.p1 fails validation.
(AGC)	 TC	59525-59947	GT	AGG
Valid prediction for GeneMark_model.23283_t
Valid prediction for Augustus_model.g9267.t1
Valid prediction for GlimmerHMM_glimmerT_13893-T1
Valid prediction for GeneMark_model.23282_t
Valid prediction for GlimmerHMM_glimmerT_13892-T1
Valid prediction for Augustus_model.g9271.t1
Valid prediction for snap_scaffold_5-snap.3356-T1
Valid prediction for GeneMark_model.23277_t
Valid prediction for GlimmerHMM_glimmerT_13881-T1
Valid prediction for GeneMark_model.23273_t
Valid prediction for GlimmerHMM_glimmerT_13887-T1
Valid prediction for Augustus_model.g9266.t1
Valid prediction for GlimmerHMM_glimmerT_13878-T1
Valid prediction for GlimmerHMM_glimmerT_13880-T1
Valid prediction for snap_scaffold_5-snap.3331-T1
Valid prediction for snap_scaffold_5-snap.3357-T1
Valid prediction for GeneMark_model.23274_t
Valid prediction for snap_scaffold_5-snap.3352-T1
Valid prediction for snap_scaffold_5-snap.3345-T1
Valid prediction for snap_scaffold_5-snap.3341-T1
Valid prediction for snap_scaffold_5-snap.3358-T1
Valid prediction for GeneMark_model.23272_t
Valid prediction for GeneMark_model.23291_t
Valid prediction for snap_scaffold_5-snap.3346-T1
Valid prediction for snap_scaffold_5-snap.3330-T1
Valid prediction for GlimmerHMM_glimmerT_13894-T1
Valid prediction for GlimmerHMM_glimmerT_13889-T1
Valid prediction for GeneMark_model.23285_t
Valid prediction for GlimmerHMM_glimmerT_13885-T1
Valid prediction for GeneMark_model.23271_t
Valid prediction for GeneMark_model.23289_t
Valid prediction for snap_scaffold_5-snap.3348-T1
Valid prediction for snap_scaffold_5-snap.3355-T1
Valid prediction for Augustus_model.g9276.t1
Valid prediction for GeneMark_model.23269_t
Valid prediction for snap_scaffold_5-snap.3360-T1
Valid prediction for GlimmerHMM_glimmerT_13886-T1
Valid prediction for snap_scaffold_5-snap.3339-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.23290_t
Valid prediction for Augustus_model.g9272.t1
Couldn't classify 84028, 84202
Sorry, prediction pasa_asmbl_46191.p1 fails validation.
(ATG)	 TA	82976-83202	GT	AGG
(CAG)	 AG	84028-84202	GT	TGG
-recovered pasa_asmbl_46191.p1, initial, 82976, 83202
-recovered pasa_asmbl_46191.p1, internal, 84028, 84202
Valid prediction for GlimmerHMM_glimmerT_13879-T1
Valid prediction for snap_scaffold_5-snap.3351-T1
Valid prediction for GeneMark_model.23270_t
Valid prediction for GeneMark_model.23286_t
Valid prediction for GeneMark_model.23284_t
Couldn't classify 90746, 90829
Couldn't classify 92074, 92215
Sorry, prediction pasa_asmbl_46335.p1 fails validation.
(GAA)	 AG	90746-90829	GT	AGG
(GGG)	 AG	91185-91286	GT	AGG
(GCT)	 AG	91577-91611	GT	AGG
(TTT)	 AG	92074-92215	AA	CCA
-recovered pasa_asmbl_46335.p1, internal, 90746, 90829
-recovered pasa_asmbl_46335.p1, internal, 91185, 91286
-recovered pasa_asmbl_46335.p1, internal, 91577, 91611
Valid prediction for GlimmerHMM_glimmerT_13884-T1
Valid prediction for GeneMark_model.23288_t
Valid prediction for snap_scaffold_5-snap.3340-T1
Valid prediction for Augustus_model.g9268.t1
Valid prediction for GeneMark_model.23292_t
Valid prediction for snap_scaffold_5-snap.3335-T1
Valid prediction for GlimmerHMM_glimmerT_13890-T1
Valid prediction for Augustus_model.g9275.t1
Valid prediction for GeneMark_model.23296_t
Valid prediction for GeneMark_model.23293_t
Valid prediction for snap_scaffold_5-snap.3350-T1
Valid prediction for GeneMark_model.23278_t
Valid prediction for snap_scaffold_5-snap.3361-T1
Valid prediction for HiQ_model.g9277.t1
Valid prediction for snap_scaffold_5-snap.3344-T1
Valid prediction for GeneMark_model.23276_t
Valid prediction for snap_scaffold_5-snap.3362-T1
Valid prediction for GeneMark_model.23280_t
Valid prediction for snap_scaffold_5-snap.3342-T1
Valid prediction for GlimmerHMM_glimmerT_13882-T1
Valid prediction for snap_scaffold_5-snap.3332-T1
Valid prediction for snap_scaffold_5-snap.3336-T1
Valid prediction for snap_scaffold_5-snap.3347-T1
Valid prediction for GeneMark_model.23298_t
Valid prediction for Augustus_model.g9270.t1
Valid prediction for GeneMark_model.23287_t
Valid prediction for snap_scaffold_5-snap.3354-T1
Valid prediction for GeneMark_model.23275_t
Valid prediction for snap_scaffold_5-snap.3334-T1
Valid prediction for snap_scaffold_5-snap.3333-T1
Valid prediction for GlimmerHMM_glimmerT_13891-T1
Valid prediction for snap_scaffold_5-snap.3343-T1
Valid prediction for GeneMark_model.23268_t
Valid prediction for Augustus_model.g9265.t1
Valid prediction for Augustus_model.g9274.t1
Valid prediction for CodingQuarry_transcript_52309-T1
Couldn't classify 48156, 48212
Sorry, prediction pasa_asmbl_46193.p1 fails validation.
(GGA)	 TG	48156-48212	GT	AGG
(GTG)	 AG	48681-49805	CA	AGC
-recovered pasa_asmbl_46193.p1, terminal, 48681, 49805
Valid prediction for GeneMark_model.23294_t
Valid prediction for snap_scaffold_5-snap.3338-T1
Valid prediction for Augustus_model.g9269.t1
Valid prediction for snap_scaffold_5-snap.3353-T1
Valid prediction for Augustus_model.g9273.t1
Valid prediction for snap_scaffold_5-snap.3359-T1
Valid prediction for GeneMark_model.23279_t
Valid prediction for pasa_asmbl_46189.p1
Valid prediction for snap_scaffold_5-snap.3349-T1
Valid prediction for GlimmerHMM_glimmerT_13888-T1
Valid prediction for pasa_asmbl_46195.p1
Couldn't classify 46681, 46960
Couldn't classify 47133, 47452
Sorry, prediction pasa_asmbl_46194.p1 fails validation.
(GGC)	 TG	46681-46960	GC	CGG
(GCC)	 AG	47133-47452	CA	GCC

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 50535, rend_intergenic: 48348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96358, rend_intergenic: 93760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105097, rend_intergenic: 101501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107180, rend_intergenic: 106367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112487, rend_intergenic: 107480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123072, rend_intergenic: 120479  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129167, rend_intergenic: 125622  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 171814
-exon list size: 364


building trellis

0.3    
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1.9    
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3.3    
3.6    
3.8    
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5.7    
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7.1    
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7.9    
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10.4    
10.7    
10.9    
11.2    
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11.7    
12.0    
12.3    
12.6    
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13.4    
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14.5    
14.8    
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15.3    
15.6    
15.8    
16.1    
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16.9    
17.2    
17.5    
17.8    
18.0    
18.3    
18.6    
18.9    
19.1    
19.4    
19.7    
19.9    
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20.8    
21.0    
21.3    
21.6    
21.9    
22.1    
22.4    
22.7    
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23.2    
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24.6    
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25.1    
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25.7    
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26.8    
27.0    
27.3    
27.6    
27.9    
28.1    
28.4    
28.7    
29.0    
29.2    
29.5    
29.8    
30.1    
30.3    
30.6    
30.9    
31.1    
31.4    
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32.2    
32.5    
32.8    
33.1    
33.3    
33.6    
33.9    
34.2    
34.4    
34.7    
35.0    
35.2    
35.5    
35.8    
36.1    
36.3    
36.6    
36.9    
37.2    
37.4    
37.7    
38.0    
38.3    
38.5    
38.8    
39.1    
39.3    
39.6    
39.9    
40.2    
40.4    
40.7    
41.0    
41.3    
41.5    
41.8    
42.1    
42.3    
42.6    
42.9    
43.2    
43.4    
43.7    
44.0    
44.3    
44.5    
44.8    
45.1    
45.4    
45.6    
45.9    
46.2    
46.4    
46.7    
47.0    
47.3    
47.5    
47.8    
48.1    
48.4    
48.6    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.4    
51.6    
51.9    
52.2    
52.5    
52.7    
53.0    
53.3    
53.6    
53.8    
54.1    
54.4    
54.6    
54.9    
55.2    
55.5    
55.7    
56.0    
56.3    
56.6    
56.8    
57.1    
57.4    
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57.9    
58.2    
58.5    
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59.0    
59.3    
59.6    
59.8    
60.1    
60.4    
60.7    
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61.2    
61.5    
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62.0    
62.3    
62.6    
62.8    
63.1    
63.4    
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64.2    
64.5    
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65.0    
65.3    
65.6    
65.8    
66.1    
66.4    
66.7    
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67.2    
67.5    
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68.0    
68.3    
68.6    
68.9    
69.1    
69.4    
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70.2    
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71.0    
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71.6    
71.9    
72.1    
72.4    
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73.0    
73.2    
73.5    
73.8    
74.0    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
76.0    
76.2    
76.5    
76.8    
77.0    
77.3    
77.6    
77.9    
78.1    
78.4    
78.7    
79.0    
79.2    
79.5    
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80.1    
80.3    
80.6    
80.9    
81.1    
81.4    
81.7    
82.0    
82.2    
82.5    
82.8    
83.1    
83.3    
83.6    
83.9    
84.2    
84.4    
84.7    
85.0    
85.2    
85.5    
85.8    
86.1    
86.3    
86.6    
86.9    
87.2    
87.4    
87.7    
88.0    
88.3    
88.5    
88.8    
89.1    
89.3    
89.6    
89.9    
90.2    
90.4    
90.7    
91.0    
91.3    
91.5    
91.8    
92.1    
92.3    
92.6    
92.9    
93.2    
93.4    
93.7    
94.0    
94.3    
94.5    
94.8    
95.1    
95.4    
95.6    
95.9    
96.2    
96.4    
96.7    
97.0    
97.3    
97.5    
97.8    
98.1    
98.4    
98.6    
98.9    
99.2    
99.5    
99.7    
-found 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 50535, rend_intergenic: 48348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96358, rend_intergenic: 93760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105097, rend_intergenic: 101501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107180, rend_intergenic: 106367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112487, rend_intergenic: 107480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123072, rend_intergenic: 120479  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129167, rend_intergenic: 125622  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support