-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_2337539-2501683

-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.479-T1
Valid prediction for Augustus_model.g7782.t1
Valid prediction for GeneMark_model.19851_t
Valid prediction for GeneMark_model.19847_t
Valid prediction for Augustus_model.g7778.t1
Valid prediction for GlimmerHMM_glimmerT_11825-T1
Valid prediction for snap_scaffold_5-snap.492-T1
Valid prediction for snap_scaffold_5-snap.467-T1
Valid prediction for GeneMark_model.19875_t
Valid prediction for snap_scaffold_5-snap.463-T1
Valid prediction for GlimmerHMM_glimmerT_11830-T1
Valid prediction for GeneMark_model.19849_t
Valid prediction for snap_scaffold_5-snap.470-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.19869_t
Valid prediction for snap_scaffold_5-snap.483-T1
Valid prediction for GeneMark_model.19881_t
Valid prediction for HiQ_model.g7781.t1
Valid prediction for GlimmerHMM_glimmerT_11817-T1
Valid prediction for snap_scaffold_5-snap.493-T1
Valid prediction for snap_scaffold_5-snap.472-T1
Valid prediction for snap_scaffold_5-snap.464-T1
Valid prediction for GeneMark_model.19878_t
Valid prediction for Augustus_model.g7779.t1
Valid prediction for snap_scaffold_5-snap.468-T1
Valid prediction for Augustus_model.g7785.t1
Valid prediction for Augustus_model.g7775.t1
Valid prediction for GeneMark_model.19880_t
Valid prediction for snap_scaffold_5-snap.476-T1
Valid prediction for GlimmerHMM_glimmerT_11819-T1
Valid prediction for snap_scaffold_5-snap.495-T1
Valid prediction for snap_scaffold_5-snap.475-T1
Valid prediction for GeneMark_model.19862_t
Valid prediction for GlimmerHMM_glimmerT_11824-T1
Valid prediction for snap_scaffold_5-snap.489-T1
Valid prediction for GeneMark_model.19841_t
Valid prediction for GeneMark_model.19857_t
Valid prediction for snap_scaffold_5-snap.473-T1
Valid prediction for GeneMark_model.19858_t
Valid prediction for GlimmerHMM_glimmerT_11822-T1
Valid prediction for snap_scaffold_5-snap.477-T1
Couldn't classify 53090, 53298
Sorry, prediction pasa_asmbl_43827.p1 fails validation.
(TCC)	 CC	53090-53298	GT	AGG
(GCT)	 AG	54441-54663	GG	GAG
-recovered pasa_asmbl_43827.p1, terminal, 54441, 54663
Valid prediction for GlimmerHMM_glimmerT_11829-T1
Valid prediction for snap_scaffold_5-snap.487-T1
Valid prediction for GeneMark_model.19867_t
Valid prediction for snap_scaffold_5-snap.466-T1
Valid prediction for GlimmerHMM_glimmerT_11820-T1
Valid prediction for snap_scaffold_5-snap.461-T1
Valid prediction for GlimmerHMM_glimmerT_11821-T1
Valid prediction for GlimmerHMM_glimmerT_11823-T1
Valid prediction for GeneMark_model.19843_t
Valid prediction for Augustus_model.g7774.t1
Valid prediction for GlimmerHMM_glimmerT_11834-T1
Valid prediction for Augustus_model.g7784.t1
Valid prediction for GeneMark_model.19864_t
Valid prediction for snap_scaffold_5-snap.478-T1
Valid prediction for GeneMark_model.19846_t
Valid prediction for Augustus_model.g7780.t1
Valid prediction for GlimmerHMM_glimmerT_11832-T1
Valid prediction for Augustus_model.g7783.t1
Valid prediction for GeneMark_model.19855_t
Valid prediction for snap_scaffold_5-snap.462-T1
Valid prediction for GlimmerHMM_glimmerT_11828-T1
Valid prediction for GeneMark_model.19840_t
Couldn't classify 52919, 53032
Sorry, prediction pasa_asmbl_43826.p1 fails validation.
(ATG)	 AA	50944-51053	GT	AGG
(GAA)	 AG	51518-51638	GT	AGG
(AAC)	 AG	51762-51959	GT	ATG
(GAA)	 AG	52178-52357	GT	GGG
(AGT)	 AG	52919-53032	TC	CCT
-recovered pasa_asmbl_43826.p1, initial, 50944, 51053
-recovered pasa_asmbl_43826.p1, internal, 51518, 51638
-recovered pasa_asmbl_43826.p1, internal, 51762, 51959
-recovered pasa_asmbl_43826.p1, internal, 52178, 52357
Valid prediction for GlimmerHMM_glimmerT_11826-T1
Valid prediction for GeneMark_model.19871_t
Valid prediction for GlimmerHMM_glimmerT_11818-T1
Valid prediction for GeneMark_model.19877_t
Valid prediction for GeneMark_model.19876_t
Valid prediction for GeneMark_model.19873_t
Valid prediction for GeneMark_model.19835_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.19866_t
Valid prediction for GeneMark_model.19853_t
Valid prediction for GeneMark_model.19879_t
Valid prediction for GeneMark_model.19859_t
Valid prediction for GeneMark_model.19868_t
Valid prediction for snap_scaffold_5-snap.481-T1
Valid prediction for snap_scaffold_5-snap.482-T1
Valid prediction for Augustus_model.g7786.t1
Valid prediction for snap_scaffold_5-snap.488-T1
Valid prediction for GeneMark_model.19850_t
Valid prediction for snap_scaffold_5-snap.474-T1
Valid prediction for snap_scaffold_5-snap.485-T1
Valid prediction for snap_scaffold_5-snap.494-T1
Valid prediction for snap_scaffold_5-snap.484-T1
Valid prediction for Augustus_model.g7777.t1
Valid prediction for GeneMark_model.19856_t
Valid prediction for snap_scaffold_5-snap.490-T1
Valid prediction for GeneMark_model.19845_t
Valid prediction for snap_scaffold_5-snap.480-T1
Valid prediction for snap_scaffold_5-snap.471-T1
Valid prediction for snap_scaffold_5-snap.491-T1
Valid prediction for snap_scaffold_5-snap.486-T1
Valid prediction for GeneMark_model.19837_t
Valid prediction for GeneMark_model.19860_t
Valid prediction for GeneMark_model.19863_t
Valid prediction for snap_scaffold_5-snap.465-T1
Valid prediction for GeneMark_model.19848_t
Valid prediction for GeneMark_model.19861_t
Valid prediction for GeneMark_model.19838_t
Valid prediction for GeneMark_model.19874_t
Valid prediction for GeneMark_model.19870_t
Valid prediction for GeneMark_model.19872_t
Valid prediction for GeneMark_model.19842_t
Valid prediction for GeneMark_model.19834_t
Valid prediction for GlimmerHMM_glimmerT_11827-T1
Valid prediction for GlimmerHMM_glimmerT_11835-T1
Valid prediction for GlimmerHMM_glimmerT_11833-T1
Valid prediction for GeneMark_model.19844_t
Valid prediction for GlimmerHMM_glimmerT_11831-T1
Valid prediction for GlimmerHMM_glimmerT_11816-T1
Valid prediction for Augustus_model.g7776.t1
Valid prediction for snap_scaffold_5-snap.469-T1
Valid prediction for GeneMark_model.19865_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15304, rend_intergenic: 12039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28071, rend_intergenic: 24736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29955, rend_intergenic: 29605  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33631, rend_intergenic: 30064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42914, rend_intergenic: 34874  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98221, rend_intergenic: 80397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121085, rend_intergenic: 104535  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127549, rend_intergenic: 121447  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150462, rend_intergenic: 140061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157388, rend_intergenic: 156186  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159856, rend_intergenic: 158826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 164145
-exon list size: 586


building trellis

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40.8    
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42.0    
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48.6    
48.8    
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49.1    
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55.3    
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56.1    
56.3    
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56.8    
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57.3    
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58.8    
59.0    
59.2    
59.4    
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60.0    
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60.9    
61.1    
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62.2    
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64.1    
64.3    
64.5    
64.6    
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66.8    
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69.0    
69.2    
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73.6    
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74.0    
74.1    
74.3    
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74.8    
75.0    
75.2    
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76.2    
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77.0    
77.2    
77.4    
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77.9    
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78.2    
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78.6    
78.7    
78.9    
79.1    
79.3    
79.4    
79.6    
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80.3    
80.4    
80.6    
80.8    
81.0    
81.1    
81.3    
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81.6    
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82.0    
82.1    
82.3    
82.5    
82.7    
82.8    
83.0    
83.2    
83.3    
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84.0    
84.2    
84.4    
84.5    
84.7    
84.9    
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85.2    
85.4    
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85.9    
86.1    
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86.9    
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90.1    
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90.5    
90.6    
90.8    
91.0    
91.2    
91.3    
91.5    
91.7    
91.8    
92.0    
92.2    
92.3    
92.5    
92.7    
92.9    
93.0    
93.2    
93.4    
93.5    
93.7    
93.9    
94.0    
94.2    
94.4    
94.6    
94.7    
94.9    
95.1    
95.2    
95.4    
95.6    
95.7    
95.9    
96.1    
96.3    
96.4    
96.6    
96.8    
96.9    
97.1    
97.3    
97.4    
97.6    
97.8    
98.0    
98.1    
98.3    
98.5    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 15304, rend_intergenic: 12039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28071, rend_intergenic: 24736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29955, rend_intergenic: 29605  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33631, rend_intergenic: 30064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42914, rend_intergenic: 34874  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98221, rend_intergenic: 80397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121085, rend_intergenic: 104535  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127549, rend_intergenic: 121447  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150462, rend_intergenic: 140061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157388, rend_intergenic: 156186  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159856, rend_intergenic: 158826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 12748
-exon list size: 28


building trellis

3.3    
6.7    
10.0    
13.3    
16.7    
20.0    
23.3    
26.7    
30.0    
33.3    
36.7    
40.0    
43.3    
46.7    
50.0    
53.3    
56.7    
60.0    
63.3    
66.7    
70.0    
73.3    
76.7    
80.0    
83.3    
86.7    
90.0    
93.3    
96.7    
-found 1 predictions from path traversal

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