-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_23/scaffold_23_4987756-5286216

-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 GlimmerHMM_glimmerT_52203-T1
Valid prediction for GeneMark_model.90581_t
Valid prediction for Augustus_model.g35104.t1
Valid prediction for snap_scaffold_23-snap.909-T1
Valid prediction for snap_scaffold_23-snap.947-T1
Valid prediction for snap_scaffold_23-snap.911-T1
Valid prediction for Augustus_model.g35118.t1
Valid prediction for snap_scaffold_23-snap.912-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for GeneMark_model.90570_t
Valid prediction for GeneMark_model.90567_t
Valid prediction for snap_scaffold_23-snap.945-T1
Valid prediction for GlimmerHMM_glimmerT_52226-T1
Valid prediction for Augustus_model.g35108.t1
Valid prediction for snap_scaffold_23-snap.940-T1
Valid prediction for GlimmerHMM_glimmerT_52200-T1
Valid prediction for GeneMark_model.90592_t
Valid prediction for GlimmerHMM_glimmerT_52196-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_35583-T1
Valid prediction for Augustus_model.g35116.t1
Valid prediction for GlimmerHMM_glimmerT_52195-T1
Valid prediction for snap_scaffold_23-snap.919-T1
Valid prediction for GlimmerHMM_glimmerT_52228-T1
Valid prediction for Augustus_model.g35126.t1
Valid prediction for snap_scaffold_23-snap.916-T1
Valid prediction for Augustus_model.g35111.t1
Valid prediction for Augustus_model.g35110.t1
Valid prediction for snap_scaffold_23-snap.928-T1
Valid prediction for GlimmerHMM_glimmerT_52206-T1
Valid prediction for GlimmerHMM_glimmerT_52232-T1
Valid prediction for Augustus_model.g35113.t1
Valid prediction for Augustus_model.g35105.t1
Valid prediction for snap_scaffold_23-snap.926-T1
Valid prediction for GlimmerHMM_glimmerT_52216-T1
Valid prediction for GlimmerHMM_glimmerT_52197-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for GeneMark_model.90594_t
Valid prediction for GlimmerHMM_glimmerT_52227-T1
Valid prediction for GlimmerHMM_glimmerT_52211-T1
Valid prediction for snap_scaffold_23-snap.920-T1
Valid prediction for GeneMark_model.90596_t
Valid prediction for GeneMark_model.90574_t
Valid prediction for Augustus_model.g35127.t1
Valid prediction for snap_scaffold_23-snap.948-T1
Valid prediction for GlimmerHMM_glimmerT_52204-T1
Valid prediction for GlimmerHMM_glimmerT_52193-T1
Couldn't classify 13608, 13895
Sorry, prediction GeneMark_model.90566_t fails validation.
(GCT)	 AG	13608-13895	GT	GGG
(GTG)	 AG	15819-15892	TG	AAT
-recovered GeneMark_model.90566_t, terminal, 15819, 15892
-recovered GeneMark_model.90566_t, internal, 13608, 13895
Valid prediction for GeneMark_model.90591_t
Valid prediction for Augustus_model.g35123.t1
Valid prediction for Augustus_model.g35107.t1
Valid prediction for GlimmerHMM_glimmerT_52208-T1
Valid prediction for snap_scaffold_23-snap.944-T1
Valid prediction for GeneMark_model.90571_t
Couldn't classify 57015, 57203
Sorry, prediction pasa_asmbl_30847.p1 fails validation.
(GGT)	 AA	57015-57203	GT	AGG
(GGT)	 AG	58458-58508	GT	AGG
(GTG)	 AG	59586-59633	GT	AGG
(GTA)	 AG	59977-60054	TG	AAT
-recovered pasa_asmbl_30847.p1, terminal, 59977, 60054
-recovered pasa_asmbl_30847.p1, internal, 58458, 58508
-recovered pasa_asmbl_30847.p1, internal, 59586, 59633
Valid prediction for snap_scaffold_23-snap.918-T1
Valid prediction for GlimmerHMM_glimmerT_52214-T1
Valid prediction for Augustus_model.g35131.t1
Valid prediction for snap_scaffold_23-snap.917-T1
Valid prediction for GeneMark_model.90569_t
Valid prediction for snap_scaffold_23-snap.910-T1
Valid prediction for snap_scaffold_23-snap.921-T1
Valid prediction for snap_scaffold_23-snap.915-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for Augustus_model.g35130.t1
Valid prediction for GlimmerHMM_glimmerT_52231-T1
Valid prediction for GeneMark_model.90593_t
Valid prediction for GlimmerHMM_glimmerT_52218-T1
Valid prediction for pasa_asmbl_30844.p1
Valid prediction for GeneMark_model.90568_t
Valid prediction for GeneMark_model.90586_t
Valid prediction for snap_scaffold_23-snap.949-T1
Valid prediction for Augustus_model.g35128.t1
Valid prediction for snap_scaffold_23-snap.950-T1
Valid prediction for GeneMark_model.90576_t
Valid prediction for snap_scaffold_23-snap.946-T1
Valid prediction for snap_scaffold_23-snap.914-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_23-snap.935-T1
Valid prediction for snap_scaffold_23-snap.942-T1
Valid prediction for GeneMark_model.90588_t
Valid prediction for pasa_asmbl_31623.p1
Valid prediction for HiQ_model.g35115.t1
Valid prediction for GeneMark_model.90595_t
Valid prediction for GeneMark_model.90589_t
Valid prediction for CodingQuarry_transcript_35586-T1
Valid prediction for snap_scaffold_23-snap.937-T1
Valid prediction for snap_scaffold_23-snap.923-T1
Valid prediction for snap_scaffold_23-snap.924-T1
Valid prediction for snap_scaffold_23-snap.939-T1
Valid prediction for HiQ_model.g35119.t1
Valid prediction for GlimmerHMM_glimmerT_52224-T1
Valid prediction for GlimmerHMM_glimmerT_52223-T1
Valid prediction for Augustus_model.g35109.t1
Valid prediction for snap_scaffold_23-snap.941-T1
Valid prediction for GlimmerHMM_glimmerT_52213-T1
Valid prediction for GlimmerHMM_glimmerT_52222-T1
Valid prediction for GeneMark_model.90590_t
Valid prediction for Augustus_model.g35117.t1
Valid prediction for GlimmerHMM_glimmerT_52225-T1
Valid prediction for HiQ_model.g35106.t1
Couldn't classify 110656, 110740
Sorry, prediction pasa_asmbl_31615.p1 fails validation.
(ATG)	 CC	96667-96837	GT	CGG
(CCC)	 AG	97648-97843	GT	AGG
(GTT)	 AG	98591-98681	GT	AGG
(GAG)	 AG	100828-100913	GT	AGG
(AGT)	 AG	103130-103284	GT	AGG
(ATT)	 AG	103523-103624	GT	AGG
(GTG)	 AG	106150-106311	GT	AGG
(CAA)	 AG	108424-108545	GT	GGG
(GAA)	 AG	108668-108769	GT	ATG
(GAT)	 AG	108905-108991	GT	AGG
(GTT)	 AG	109110-109185	GT	AGG
(GAA)	 AG	109290-109399	GT	ATG
(GTA)	 AG	110656-110740	GG	AAG
-recovered pasa_asmbl_31615.p1, initial, 96667, 96837
-recovered pasa_asmbl_31615.p1, internal, 97648, 97843
-recovered pasa_asmbl_31615.p1, internal, 98591, 98681
-recovered pasa_asmbl_31615.p1, internal, 100828, 100913
-recovered pasa_asmbl_31615.p1, internal, 103130, 103284
-recovered pasa_asmbl_31615.p1, internal, 103523, 103624
-recovered pasa_asmbl_31615.p1, internal, 106150, 106311
-recovered pasa_asmbl_31615.p1, internal, 108424, 108545
-recovered pasa_asmbl_31615.p1, internal, 108668, 108769
-recovered pasa_asmbl_31615.p1, internal, 108905, 108991
-recovered pasa_asmbl_31615.p1, internal, 109110, 109185
-recovered pasa_asmbl_31615.p1, internal, 109290, 109399
Valid prediction for pasa_asmbl_31603.p1
Valid prediction for snap_scaffold_23-snap.934-T1
Couldn't classify 64900, 64975
Couldn't classify 74153, 74248
Sorry, prediction pasa_asmbl_31621.p1 fails validation.
(GCC)	 CG	64900-64975	GT	AGG
(GGT)	 AG	67375-67504	GT	AAG
(CTC)	 AG	69084-69200	GT	ATG
(ATT)	 AG	69376-69448	GT	AGG
(GTG)	 AG	69790-70000	GT	AGG
(GTT)	 AG	70396-70599	GT	TGG
(GTG)	 AG	71058-71176	GT	AGG
(GAG)	 AG	74153-74248	AG	AAA
-recovered pasa_asmbl_31621.p1, internal, 67375, 67504
-recovered pasa_asmbl_31621.p1, internal, 69084, 69200
-recovered pasa_asmbl_31621.p1, internal, 69376, 69448
-recovered pasa_asmbl_31621.p1, internal, 69790, 70000
-recovered pasa_asmbl_31621.p1, internal, 70396, 70599
-recovered pasa_asmbl_31621.p1, internal, 71058, 71176
Valid prediction for Augustus_model.g35129.t1
Valid prediction for GeneMark_model.90584_t
Valid prediction for GlimmerHMM_glimmerT_52207-T1
Valid prediction for Augustus_model.g35112.t1
Valid prediction for snap_scaffold_23-snap.932-T1
Valid prediction for GeneMark_model.90580_t
Valid prediction for snap_scaffold_23-snap.913-T1
Couldn't classify 58369, 58472
Couldn't classify 59978, 60027
Sorry, prediction pasa_asmbl_31622.p1 fails validation.
(GCA)	 AG	58369-58472	GT	GGG
(GGG)	 AG	59560-59756	GT	AGG
(GTC)	 AG	59978-60027	AT	AGA
-recovered pasa_asmbl_31622.p1, internal, 58369, 58472
-recovered pasa_asmbl_31622.p1, internal, 59560, 59756
Valid prediction for snap_scaffold_23-snap.927-T1
Valid prediction for pasa_asmbl_31605.p1
Valid prediction for GlimmerHMM_glimmerT_52201-T1
Couldn't classify 201649, 201888
Couldn't classify 207611, 207771
Sorry, prediction pasa_asmbl_31600.p1 fails validation.
(CAG)	 GC	201649-201888	GT	AGG
(GGT)	 AG	202544-202704	GT	CTG
(TAT)	 AG	203891-204029	GT	AGG
(TTA)	 AG	204247-204325	GT	CGG
(TGG)	 AG	204638-204675	GT	CTG
(CAA)	 AG	205651-205722	GT	AGG
(AGG)	 AG	207264-207342	GT	TGG
(ATG)	 AG	207611-207771	TA	AGT
-recovered pasa_asmbl_31600.p1, internal, 202544, 202704
-recovered pasa_asmbl_31600.p1, internal, 203891, 204029
-recovered pasa_asmbl_31600.p1, internal, 204247, 204325
-recovered pasa_asmbl_31600.p1, internal, 204638, 204675
-recovered pasa_asmbl_31600.p1, internal, 205651, 205722
-recovered pasa_asmbl_31600.p1, internal, 207264, 207342
Valid prediction for GlimmerHMM_glimmerT_52210-T1
Valid prediction for GeneMark_model.90587_t
Valid prediction for GeneMark_model.90578_t
Valid prediction for GlimmerHMM_glimmerT_52221-T1
Valid prediction for GeneMark_model.90572_t
Valid prediction for GeneMark_model.90583_t
Valid prediction for GlimmerHMM_glimmerT_52202-T1
Valid prediction for GlimmerHMM_glimmerT_52230-T1
Valid prediction for Augustus_model.g35121.t1
Valid prediction for GlimmerHMM_glimmerT_52219-T1
Valid prediction for GlimmerHMM_glimmerT_52194-T1
Valid prediction for snap_scaffold_23-snap.936-T1
Valid prediction for Augustus_model.g35125.t1
Valid prediction for GlimmerHMM_glimmerT_52215-T1
Couldn't classify 80648, 80699
Sorry, prediction pasa_asmbl_31617.p1 fails validation.
(GCT)	 AA	80648-80699	GT	AGG
(AAA)	 AG	82402-82713	GT	AGG
(ACG)	 AG	83132-83191	GT	AGG
(GCA)	 AG	85014-85198	GA	AAG
-recovered pasa_asmbl_31617.p1, terminal, 85014, 85198
-recovered pasa_asmbl_31617.p1, internal, 82402, 82713
-recovered pasa_asmbl_31617.p1, internal, 83132, 83191
Valid prediction for snap_scaffold_23-snap.925-T1
Valid prediction for snap_scaffold_23-snap.933-T1
Couldn't classify 215706, 215914
Sorry, prediction pasa_asmbl_31599.p1 fails validation.
(ACA)	 GG	215706-215914	GT	AAG
(GCA)	 AG	216168-216357	GT	AGG
(GCC)	 AG	217126-217266	GT	AGG
(GGT)	 AG	219887-219999	GT	AGG
(TGT)	 AG	220197-220269	TC	GAT
-recovered pasa_asmbl_31599.p1, terminal, 220197, 220269
-recovered pasa_asmbl_31599.p1, internal, 216168, 216357
-recovered pasa_asmbl_31599.p1, internal, 217126, 217266
-recovered pasa_asmbl_31599.p1, internal, 219887, 219999
Valid prediction for GeneMark_model.90585_t
Valid prediction for GlimmerHMM_glimmerT_52205-T1
Valid prediction for CodingQuarry_transcript_35585-T1
Valid prediction for GeneMark_model.90573_t
Valid prediction for GlimmerHMM_glimmerT_52229-T1
Valid prediction for GlimmerHMM_glimmerT_52209-T1
Valid prediction for pasa_asmbl_31614.p1
Valid prediction for GlimmerHMM_glimmerT_52212-T1
Valid prediction for CodingQuarry_transcript_35584-T1
Valid prediction for snap_scaffold_23-snap.943-T1
Valid prediction for GlimmerHMM_glimmerT_52220-T1
Valid prediction for snap_scaffold_23-snap.930-T1
Valid prediction for Augustus_model.g35120.t1
Valid prediction for GlimmerHMM_glimmerT_52199-T1
Valid prediction for snap_scaffold_23-snap.922-T1
Valid prediction for Augustus_model.g35114.t1
Valid prediction for GlimmerHMM_glimmerT_52198-T1
Valid prediction for Augustus_model.g35124.t1
Valid prediction for snap_scaffold_23-snap.931-T1
Valid prediction for snap_scaffold_23-snap.929-T1
Valid prediction for GeneMark_model.90575_t
Valid prediction for snap_scaffold_23-snap.938-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g35122.t1
Valid prediction for GlimmerHMM_glimmerT_52217-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)
-building DP trellis

-building trellis in range 1 - 298461
-exon list size: 485


building trellis

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32.9    
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33.9    
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34.9    
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43.9    
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47.8    
48.0    
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48.9    
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49.3    
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49.7    
49.9    
50.1    
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50.5    
50.7    
50.9    
51.1    
51.3    
51.5    
51.7    
52.0    
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52.8    
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53.8    
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54.8    
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55.2    
55.4    
55.6    
55.9    
56.1    
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56.5    
56.7    
56.9    
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57.3    
57.5    
57.7    
57.9    
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58.3    
58.5    
58.7    
58.9    
59.1    
59.3    
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59.8    
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60.6    
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61.6    
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63.9    
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64.3    
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64.9    
65.1    
65.3    
65.5    
65.7    
65.9    
66.1    
66.3    
66.5    
66.7    
66.9    
67.1    
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67.6    
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68.0    
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68.8    
69.0    
69.2    
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73.9    
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75.2    
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75.6    
75.8    
76.0    
76.2    
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76.6    
76.8    
77.0    
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78.9    
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79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.1    
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82.3    
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82.8    
83.0    
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83.8    
84.0    
84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.6    
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86.0    
86.2    
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86.9    
87.1    
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87.5    
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87.9    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
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95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 38 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 38 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 13204
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 279670 - 298461
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support
	-no exons in range 288264 - 298461