-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_5411343-5663318

-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_3-snap.1178-T1
Valid prediction for GeneMark_model.11079_t
Valid prediction for snap_scaffold_3-snap.1174-T1
Valid prediction for snap_scaffold_3-snap.1158-T1
Valid prediction for GlimmerHMM_glimmerT_6697-T1
Valid prediction for GlimmerHMM_glimmerT_6708-T1
Valid prediction for GlimmerHMM_glimmerT_6705-T1
Valid prediction for GeneMark_model.11104_t
Valid prediction for snap_scaffold_3-snap.1184-T1
Valid prediction for Augustus_model.g4377.t1
Valid prediction for snap_scaffold_3-snap.1165-T1
Valid prediction for GlimmerHMM_glimmerT_6694-T1
Valid prediction for GeneMark_model.11077_t
Valid prediction for Augustus_model.g4378.t1
Valid prediction for snap_scaffold_3-snap.1181-T1
Valid prediction for Augustus_model.g4386.t1
Valid prediction for snap_scaffold_3-snap.1185-T1
Valid prediction for snap_scaffold_3-snap.1180-T1
Valid prediction for Augustus_model.g4385.t1
Valid prediction for GlimmerHMM_glimmerT_6703-T1
Valid prediction for snap_scaffold_3-snap.1182-T1
Valid prediction for snap_scaffold_3-snap.1183-T1
Valid prediction for snap_scaffold_3-snap.1175-T1
Valid prediction for GlimmerHMM_glimmerT_6712-T1
Valid prediction for snap_scaffold_3-snap.1167-T1
Valid prediction for GeneMark_model.11107_t
Valid prediction for snap_scaffold_3-snap.1164-T1
Valid prediction for GlimmerHMM_glimmerT_6699-T1
Valid prediction for Augustus_model.g4380.t1
Valid prediction for GeneMark_model.11091_t
Valid prediction for GeneMark_model.11096_t
Valid prediction for GlimmerHMM_glimmerT_6707-T1
Valid prediction for GlimmerHMM_glimmerT_6698-T1
Valid prediction for GlimmerHMM_glimmerT_6709-T1
Couldn't classify 249420, 249476
Couldn't classify 250030, 250106
Sorry, prediction CodingQuarry_transcript_46052-T1 fails validation.
(ATG)	 TC	247929-247950	GT	CAG
(ACT)	 AG	248048-248167	GT	GGG
(ATA)	 AG	248542-248676	GT	TGG
(ATA)	 AG	248784-248906	GT	AGG
(TCA)	 AG	249420-249476	AC	CAA
(AGC)	 GC	250030-250106	CC	GAC
-recovered CodingQuarry_transcript_46052-T1, initial, 247929, 247950
-recovered CodingQuarry_transcript_46052-T1, internal, 248048, 248167
-recovered CodingQuarry_transcript_46052-T1, internal, 248542, 248676
-recovered CodingQuarry_transcript_46052-T1, internal, 248784, 248906
Valid prediction for GlimmerHMM_glimmerT_6710-T1
Valid prediction for GlimmerHMM_glimmerT_6711-T1
Valid prediction for GeneMark_model.11087_t
Valid prediction for snap_scaffold_3-snap.1187-T1
Valid prediction for GeneMark_model.11100_t
Valid prediction for snap_scaffold_3-snap.1166-T1
Valid prediction for snap_scaffold_3-snap.1179-T1
Valid prediction for GeneMark_model.11083_t
Valid prediction for CodingQuarry_transcript_46051-T1
Valid prediction for GlimmerHMM_glimmerT_6704-T1
Valid prediction for GlimmerHMM_glimmerT_6696-T1
Valid prediction for GeneMark_model.11101_t
Valid prediction for GlimmerHMM_glimmerT_6691-T1
Valid prediction for Augustus_model.g4381.t1
Valid prediction for GeneMark_model.11084_t
Valid prediction for GeneMark_model.11085_t
Valid prediction for GeneMark_model.11092_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 snap_scaffold_3-snap.1173-T1
Valid prediction for snap_scaffold_3-snap.1163-T1
Valid prediction for Augustus_model.g4379.t1
Valid prediction for GeneMark_model.11105_t
Valid prediction for GeneMark_model.11094_t
Valid prediction for GeneMark_model.11106_t
Valid prediction for GlimmerHMM_glimmerT_6690-T1
Valid prediction for GeneMark_model.11081_t
Valid prediction for GeneMark_model.11099_t
Valid prediction for GlimmerHMM_glimmerT_6706-T1
Valid prediction for GlimmerHMM_glimmerT_6695-T1
Valid prediction for GeneMark_model.11076_t
Valid prediction for GeneMark_model.11093_t
Valid prediction for Augustus_model.g4383.t1
Valid prediction for snap_scaffold_3-snap.1170-T1
Couldn't classify 128522, 128695
Sorry, prediction pasa_asmbl_38807.p1 fails validation.
(AAG)	 TG	128522-128695	GT	AGG
(TTG)	 AG	129352-129498	GT	AGG
(TTT)	 AG	129621-129682	GT	AAG
(GAA)	 AG	129856-130021	GT	AGG
(TCT)	 AG	130634-130708	GT	CGG
(AAA)	 AG	130807-130899	GT	ATG
(CCA)	 AG	131002-131127	GT	GGG
(GAC)	 AG	131231-131311	GT	GAG
(ACA)	 AG	131408-131451	GT	GAG
(GTA)	 AG	131774-131900	GT	TGG
(GTG)	 AG	132180-132271	GT	GAG
(TGA)	 AG	132540-132679	GT	CGG
(CTG)	 AG	132954-133114	GT	AGG
(AAA)	 AG	133219-133327	GT	AAG
(GTG)	 AG	133499-133614	GT	ACG
(AGA)	 AG	133793-133882	GT	AGG
(ACG)	 AG	134216-134336	GT	AGG
(ATG)	 AG	134634-134722	GT	AGG
(GGA)	 AG	134851-134985	GT	AGG
(GTT)	 AG	135300-135375	GT	AGG
(CCA)	 AG	135498-135625	GT	GGG
(AAC)	 AG	135926-136024	GT	AGG
(ATT)	 AG	136144-136173	CC	AGC
add_exon() Sorry, pasa_asmbl_38807.p1 134634-134722-initial-1 is invalid.
-recovered pasa_asmbl_38807.p1, initial, 134634, 134722
-recovered pasa_asmbl_38807.p1, terminal, 136144, 136173
-recovered pasa_asmbl_38807.p1, internal, 129352, 129498
-recovered pasa_asmbl_38807.p1, internal, 129621, 129682
-recovered pasa_asmbl_38807.p1, internal, 129856, 130021
-recovered pasa_asmbl_38807.p1, internal, 130634, 130708
-recovered pasa_asmbl_38807.p1, internal, 130807, 130899
-recovered pasa_asmbl_38807.p1, internal, 131002, 131127
-recovered pasa_asmbl_38807.p1, internal, 131231, 131311
-recovered pasa_asmbl_38807.p1, internal, 131408, 131451
-recovered pasa_asmbl_38807.p1, internal, 131774, 131900
-recovered pasa_asmbl_38807.p1, internal, 132180, 132271
-recovered pasa_asmbl_38807.p1, internal, 132540, 132679
-recovered pasa_asmbl_38807.p1, internal, 132954, 133114
-recovered pasa_asmbl_38807.p1, internal, 133219, 133327
-recovered pasa_asmbl_38807.p1, internal, 133499, 133614
-recovered pasa_asmbl_38807.p1, internal, 133793, 133882
-recovered pasa_asmbl_38807.p1, internal, 134216, 134336
-recovered pasa_asmbl_38807.p1, internal, 134634, 134722
-recovered pasa_asmbl_38807.p1, internal, 134851, 134985
-recovered pasa_asmbl_38807.p1, internal, 135300, 135375
-recovered pasa_asmbl_38807.p1, internal, 135498, 135625
-recovered pasa_asmbl_38807.p1, internal, 135926, 136024
Valid prediction for snap_scaffold_3-snap.1186-T1
Valid prediction for GeneMark_model.11097_t
Valid prediction for GlimmerHMM_glimmerT_6702-T1
Valid prediction for GeneMark_model.11095_t
Valid prediction for GlimmerHMM_glimmerT_6713-T1
Valid prediction for snap_scaffold_3-snap.1168-T1
Valid prediction for GeneMark_model.11080_t
Valid prediction for snap_scaffold_3-snap.1177-T1
Valid prediction for GeneMark_model.11086_t
Valid prediction for GeneMark_model.11090_t
Valid prediction for Augustus_model.g4376.t1
Valid prediction for snap_scaffold_3-snap.1161-T1
Valid prediction for snap_scaffold_3-snap.1172-T1
Valid prediction for GeneMark_model.11089_t
Valid prediction for GeneMark_model.11108_t
Valid prediction for Augustus_model.g4374.t1
Valid prediction for GlimmerHMM_glimmerT_6700-T1
Valid prediction for GlimmerHMM_glimmerT_6693-T1
Valid prediction for snap_scaffold_3-snap.1162-T1
Valid prediction for GeneMark_model.11098_t
Valid prediction for GlimmerHMM_glimmerT_6701-T1
Valid prediction for snap_scaffold_3-snap.1160-T1
Valid prediction for snap_scaffold_3-snap.1176-T1
Valid prediction for pasa_asmbl_38805.p3
Valid prediction for HiQ_model.g4382.t1
Couldn't classify 120285, 120380
Sorry, prediction pasa_asmbl_38808.p1 fails validation.
(CAA)	 AG	120285-120380	GT	AGG
(GTC)	 AG	121166-121273	GT	AGG
(GCT)	 AG	122742-122890	GT	AGG
(AGT)	 AG	123076-123203	GT	AGG
(CTC)	 AG	123705-123848	GT	CAG
(GTT)	 AG	124810-124971	GT	CAG
(GCC)	 AG	125075-125282	GT	TGG
(GTT)	 AG	125406-125754	TA	AAT
-recovered pasa_asmbl_38808.p1, terminal, 125406, 125754
-recovered pasa_asmbl_38808.p1, internal, 120285, 120380
-recovered pasa_asmbl_38808.p1, internal, 121166, 121273
-recovered pasa_asmbl_38808.p1, internal, 122742, 122890
-recovered pasa_asmbl_38808.p1, internal, 123076, 123203
-recovered pasa_asmbl_38808.p1, internal, 123705, 123848
-recovered pasa_asmbl_38808.p1, internal, 124810, 124971
-recovered pasa_asmbl_38808.p1, internal, 125075, 125282
Valid prediction for Augustus_model.g4384.t1
Valid prediction for snap_scaffold_3-snap.1159-T1
Valid prediction for GeneMark_model.11088_t
Valid prediction for snap_scaffold_3-snap.1169-T1
Valid prediction for GeneMark_model.11082_t
Valid prediction for GlimmerHMM_glimmerT_6692-T1
Valid prediction for Augustus_model.g4375.t1
Valid prediction for snap_scaffold_3-snap.1171-T1
Sorry, intron length (4) is less than minimum required (10)

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

-building trellis in range 1 - 251976
-exon list size: 398


building trellis

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55.2    
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59.2    
59.5    
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60.0    
60.2    
60.5    
60.8    
61.0    
61.3    
61.5    
61.8    
62.0    
62.3    
62.5    
62.7    
63.0    
63.2    
63.5    
63.7    
64.0    
64.2    
64.5    
64.8    
65.0    
65.2    
65.5    
65.8    
66.0    
66.2    
66.5    
66.8    
67.0    
67.2    
67.5    
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68.0    
68.2    
68.5    
68.8    
69.0    
69.2    
69.5    
69.8    
70.0    
70.2    
70.5    
70.8    
71.0    
71.2    
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72.0    
72.2    
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80.0    
80.2    
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81.2    
81.5    
81.8    
82.0    
82.2    
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84.2    
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85.2    
85.5    
85.8    
86.0    
86.2    
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87.2    
87.5    
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88.2    
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89.2    
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90.2    
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90.8    
91.0    
91.2    
91.5    
91.8    
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92.2    
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93.2    
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95.2    
95.5    
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96.0    
96.2    
96.5    
96.8    
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97.2    
97.5    
97.8    
98.0    
98.2    
98.5    
98.8    
99.0    
99.2    
99.5    
99.8    
-found 24 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 13862
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-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

-building DP trellis

-building trellis in range 1 - 12523
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-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