-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_15/scaffold_15_14339217-14598595

-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.g25622.t1
Valid prediction for GlimmerHMM_glimmerT_38191-T1
Valid prediction for snap_scaffold_15-snap.2881-T1
Valid prediction for snap_scaffold_15-snap.2886-T1
Valid prediction for snap_scaffold_15-snap.2876-T1
Valid prediction for GeneMark_model.65623_t
Valid prediction for GlimmerHMM_glimmerT_38199-T1
Valid prediction for GeneMark_model.65607_t
Valid prediction for GlimmerHMM_glimmerT_38203-T1
Valid prediction for Augustus_model.g25625.t1
Valid prediction for Augustus_model.g25619.t1
Valid prediction for GlimmerHMM_glimmerT_38184-T1
Valid prediction for snap_scaffold_15-snap.2884-T1
Valid prediction for Augustus_model.g25612.t1
Valid prediction for snap_scaffold_15-snap.2903-T1
Valid prediction for GeneMark_model.65611_t
Valid prediction for GeneMark_model.65610_t
Valid prediction for GlimmerHMM_glimmerT_38198-T1
Valid prediction for snap_scaffold_15-snap.2893-T1
Valid prediction for GeneMark_model.65647_t
Valid prediction for snap_scaffold_15-snap.2898-T1
Valid prediction for GlimmerHMM_glimmerT_38202-T1
Valid prediction for snap_scaffold_15-snap.2890-T1
Valid prediction for snap_scaffold_15-snap.2910-T1
Valid prediction for Augustus_model.g25621.t1
Valid prediction for snap_scaffold_15-snap.2906-T1
Valid prediction for HiQ_model.g25615.t1
Valid prediction for GlimmerHMM_glimmerT_38186-T1
Valid prediction for snap_scaffold_15-snap.2872-T1
Valid prediction for snap_scaffold_15-snap.2909-T1
Valid prediction for GeneMark_model.65641_t
Valid prediction for snap_scaffold_15-snap.2892-T1
Valid prediction for GeneMark_model.65633_t
Valid prediction for snap_scaffold_15-snap.2879-T1
Valid prediction for snap_scaffold_15-snap.2895-T1
Valid prediction for GeneMark_model.65627_t
Valid prediction for GlimmerHMM_glimmerT_38195-T1
Valid prediction for GeneMark_model.65631_t
Valid prediction for Augustus_model.g25618.t1
Valid prediction for GeneMark_model.65644_t
Valid prediction for GlimmerHMM_glimmerT_38201-T1
Valid prediction for Augustus_model.g25623.t1
Valid prediction for GeneMark_model.65617_t
Valid prediction for snap_scaffold_15-snap.2882-T1
Valid prediction for GeneMark_model.65629_t
Valid prediction for GlimmerHMM_glimmerT_38196-T1
Valid prediction for GlimmerHMM_glimmerT_38187-T1
Valid prediction for Augustus_model.g25620.t1
Valid prediction for GeneMark_model.65609_t
Valid prediction for snap_scaffold_15-snap.2904-T1
Valid prediction for GeneMark_model.65643_t
Valid prediction for GlimmerHMM_glimmerT_38197-T1
Valid prediction for GlimmerHMM_glimmerT_38178-T1
Valid prediction for GeneMark_model.65646_t
Valid prediction for snap_scaffold_15-snap.2908-T1
Valid prediction for snap_scaffold_15-snap.2891-T1
Valid prediction for GeneMark_model.65636_t
Valid prediction for GlimmerHMM_glimmerT_38185-T1
Valid prediction for GeneMark_model.65614_t
Valid prediction for GeneMark_model.65634_t
Valid prediction for GeneMark_model.65640_t
Valid prediction for GlimmerHMM_glimmerT_38194-T1
Valid prediction for GlimmerHMM_glimmerT_38181-T1
Valid prediction for snap_scaffold_15-snap.2887-T1
Valid prediction for Augustus_model.g25611.t1
Valid prediction for CodingQuarry_transcript_18183-T1
Valid prediction for snap_scaffold_15-snap.2896-T1
Valid prediction for GeneMark_model.65618_t
Couldn't classify 170749, 171013
Sorry, prediction pasa_asmbl_14633.p1 fails validation.
(GTG)	 CT	170749-171013	GT	AGG
(GTC)	 AG	171254-171355	GT	AGG
(ACT)	 AG	171517-171672	GT	AGG
(AGA)	 AG	171786-171802	CA	AGC
-recovered pasa_asmbl_14633.p1, terminal, 171786, 171802
-recovered pasa_asmbl_14633.p1, internal, 171254, 171355
-recovered pasa_asmbl_14633.p1, internal, 171517, 171672
Valid prediction for Augustus_model.g25624.t1
Valid prediction for Augustus_model.g25616.t1
Valid prediction for GeneMark_model.65615_t
Valid prediction for GeneMark_model.65624_t
Valid prediction for snap_scaffold_15-snap.2883-T1
Valid prediction for GlimmerHMM_glimmerT_38192-T1
Valid prediction for GeneMark_model.65620_t
Valid prediction for snap_scaffold_15-snap.2894-T1
Valid prediction for GlimmerHMM_glimmerT_38200-T1
Valid prediction for snap_scaffold_15-snap.2897-T1
Valid prediction for GeneMark_model.65626_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.65639_t
Valid prediction for snap_scaffold_15-snap.2901-T1
Valid prediction for GeneMark_model.65613_t
Valid prediction for snap_scaffold_15-snap.2877-T1
Valid prediction for GeneMark_model.65645_t
Valid prediction for snap_scaffold_15-snap.2907-T1
Valid prediction for GeneMark_model.65628_t
Valid prediction for GeneMark_model.65642_t
Valid prediction for GeneMark_model.65606_t
Valid prediction for snap_scaffold_15-snap.2899-T1
Valid prediction for snap_scaffold_15-snap.2878-T1
Valid prediction for GlimmerHMM_glimmerT_38205-T1
Valid prediction for GeneMark_model.65608_t
Valid prediction for Augustus_model.g25614.t1
Valid prediction for GeneMark_model.65625_t
Valid prediction for snap_scaffold_15-snap.2885-T1
Valid prediction for GeneMark_model.65616_t
Valid prediction for snap_scaffold_15-snap.2900-T1
Valid prediction for GeneMark_model.65635_t
Couldn't classify 44319, 45269
Sorry, prediction pasa_asmbl_15739.p1 fails validation.
(GAC)	 TG	44319-45269	CA	CGC
Couldn't classify 43641, 44060
Sorry, prediction pasa_asmbl_15740.p1 fails validation.
(TCC)	 AC	43641-44060	GA	ACG
Valid prediction for GlimmerHMM_glimmerT_38190-T1
Valid prediction for GlimmerHMM_glimmerT_38207-T1
Valid prediction for GeneMark_model.65622_t
Valid prediction for GeneMark_model.65605_t
Valid prediction for GlimmerHMM_glimmerT_38182-T1
Valid prediction for Augustus_model.g25617.t1
Valid prediction for snap_scaffold_15-snap.2905-T1
Valid prediction for GlimmerHMM_glimmerT_38177-T1
Valid prediction for GlimmerHMM_glimmerT_38193-T1
Couldn't classify 45273, 48140
Sorry, prediction pasa_asmbl_15738.p1 fails validation.
(AGT)	 AT	45273-48140	GT	AGG
(GTA)	 AG	48309-48460	GT	GGG
(GTA)	 AG	49374-49549	GT	AGG
(GGA)	 AG	49845-49946	GT	AGG
(ATA)	 AG	50549-51483	GT	AGG
(GAG)	 AG	52418-53245	GA	AGG
-recovered pasa_asmbl_15738.p1, terminal, 52418, 53245
-recovered pasa_asmbl_15738.p1, internal, 48309, 48460
-recovered pasa_asmbl_15738.p1, internal, 49374, 49549
-recovered pasa_asmbl_15738.p1, internal, 49845, 49946
-recovered pasa_asmbl_15738.p1, internal, 50549, 51483
Valid prediction for GeneMark_model.65619_t
Valid prediction for GlimmerHMM_glimmerT_38204-T1
Valid prediction for snap_scaffold_15-snap.2873-T1
Valid prediction for GlimmerHMM_glimmerT_38183-T1
Valid prediction for GlimmerHMM_glimmerT_38208-T1
Valid prediction for snap_scaffold_15-snap.2902-T1
Valid prediction for GeneMark_model.65630_t
Valid prediction for snap_scaffold_15-snap.2888-T1
Valid prediction for GlimmerHMM_glimmerT_38189-T1
Valid prediction for GlimmerHMM_glimmerT_38188-T1
Valid prediction for HiQ_model.g25626.t1
Valid prediction for GeneMark_model.65632_t
Valid prediction for snap_scaffold_15-snap.2889-T1
Valid prediction for GlimmerHMM_glimmerT_38179-T1
Valid prediction for Augustus_model.g25613.t1
Valid prediction for GeneMark_model.65638_t
Valid prediction for snap_scaffold_15-snap.2875-T1
Valid prediction for snap_scaffold_15-snap.2880-T1
Valid prediction for GlimmerHMM_glimmerT_38206-T1
Valid prediction for GeneMark_model.65621_t
Valid prediction for snap_scaffold_15-snap.2874-T1
Valid prediction for GeneMark_model.65637_t
Valid prediction for GlimmerHMM_glimmerT_38180-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5431, rend_intergenic: 4371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94485, rend_intergenic: 93361  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117778, rend_intergenic: 116979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124807, rend_intergenic: 119247  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222927, rend_intergenic: 218069  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 234320, rend_intergenic: 226149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 238272, rend_intergenic: 235479  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 256250, rend_intergenic: 241638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 259379
-exon list size: 553


building trellis

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44.9    
45.0    
45.2    
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55.5    
55.7    
55.9    
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56.2    
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56.9    
57.1    
57.3    
57.5    
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57.8    
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59.1    
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61.1    
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64.1    
64.3    
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65.6    
65.8    
65.9    
66.1    
66.3    
66.5    
66.7    
66.8    
67.0    
67.2    
67.4    
67.6    
67.7    
67.9    
68.1    
68.3    
68.5    
68.6    
68.8    
69.0    
69.2    
69.4    
69.5    
69.7    
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70.3    
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70.8    
71.0    
71.2    
71.4    
71.5    
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76.8    
76.9    
77.1    
77.3    
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78.2    
78.4    
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78.7    
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79.1    
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80.4    
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81.3    
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81.6    
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82.0    
82.2    
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82.7    
82.9    
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86.1    
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86.5    
86.7    
86.8    
87.0    
87.2    
87.4    
87.6    
87.7    
87.9    
88.1    
88.3    
88.5    
88.6    
88.8    
89.0    
89.2    
89.4    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.6    
90.8    
91.0    
91.2    
91.4    
91.5    
91.7    
91.9    
92.1    
92.3    
92.4    
92.6    
92.8    
93.0    
93.2    
93.3    
93.5    
93.7    
93.9    
94.1    
94.2    
94.4    
94.6    
94.8    
95.0    
95.1    
95.3    
95.5    
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95.9    
96.0    
96.2    
96.4    
96.6    
96.8    
96.9    
97.1    
97.3    
97.5    
97.7    
97.8    
98.0    
98.2    
98.4    
98.6    
98.7    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 5431, rend_intergenic: 4371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94485, rend_intergenic: 93361  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117778, rend_intergenic: 116979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124807, rend_intergenic: 119247  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222927, rend_intergenic: 218069  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 234320, rend_intergenic: 226149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 238272, rend_intergenic: 235479  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 256250, rend_intergenic: 241638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 22402
-exon list size: 30


building trellis

3.1    
6.2    
9.4    
12.5    
15.6    
18.8    
21.9    
25.0    
28.1    
31.2    
34.4    
37.5    
40.6    
43.8    
46.9    
50.0    
53.1    
56.2    
59.4    
62.5    
65.6    
68.8    
71.9    
75.0    
78.1    
81.2    
84.4    
87.5    
90.6    
93.8    
96.9    
-found 2 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support