-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_15423275-15685957

-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.g3427.t1
Couldn't classify 72602, 72635
Couldn't classify 74006, 74135
Sorry, prediction pasa_asmbl_25058.p1 fails validation.
(TCC)	 AC	72602-72635	GT	CAG
(GCA)	 AG	72847-72942	GT	AGG
(GTG)	 AG	73121-73206	GT	AGG
(GAC)	 AG	73335-73505	GT	AAG
(CTC)	 AG	73601-73746	GT	AAG
(GGA)	 AG	74006-74135	CG	ACC
add_exon() Sorry, pasa_asmbl_25058.p1 72847-72942-terminal-1 is invalid.
-recovered pasa_asmbl_25058.p1, terminal, 72847, 72942
-recovered pasa_asmbl_25058.p1, internal, 72847, 72942
-recovered pasa_asmbl_25058.p1, internal, 73121, 73206
-recovered pasa_asmbl_25058.p1, internal, 73335, 73505
-recovered pasa_asmbl_25058.p1, internal, 73601, 73746
Valid prediction for snap_scaffold_2-snap.2991-T1
Valid prediction for GlimmerHMM_glimmerT_5099-T1
Valid prediction for GlimmerHMM_glimmerT_5097-T1
Valid prediction for GlimmerHMM_glimmerT_5069-T1
Valid prediction for snap_scaffold_2-snap.2962-T1
Valid prediction for GlimmerHMM_glimmerT_5068-T1
Valid prediction for snap_scaffold_2-snap.2955-T1
Valid prediction for GlimmerHMM_glimmerT_5100-T1
Valid prediction for GlimmerHMM_glimmerT_5091-T1
Valid prediction for snap_scaffold_2-snap.2980-T1
Valid prediction for HiQ_model.g3422.t1
Valid prediction for snap_scaffold_2-snap.2968-T1
Valid prediction for CodingQuarry_transcript_28771-T1
Valid prediction for snap_scaffold_2-snap.2956-T1
Valid prediction for pasa_asmbl_25060.p1
Valid prediction for HiQ_model.g3423.t1
Valid prediction for snap_scaffold_2-snap.2960-T1
Couldn't classify 188945, 189085
Couldn't classify 193586, 193786
Sorry, prediction pasa_asmbl_25356.p1 fails validation.
(AGG)	 GT	188945-189085	GT	AGG
(TCA)	 AG	189318-189459	GT	GGG
(GCT)	 AG	191173-191306	GT	CCG
(GAG)	 AG	191643-191765	GT	AGG
(GAG)	 AG	193586-193786	CC	AGC
-recovered pasa_asmbl_25356.p1, internal, 189318, 189459
-recovered pasa_asmbl_25356.p1, internal, 191173, 191306
-recovered pasa_asmbl_25356.p1, internal, 191643, 191765
Valid prediction for snap_scaffold_2-snap.2990-T1
Valid prediction for HiQ_model.g3428.t1
Valid prediction for GlimmerHMM_glimmerT_5065-T1
Valid prediction for snap_scaffold_2-snap.2988-T1
Valid prediction for snap_scaffold_2-snap.2975-T1
Valid prediction for CodingQuarry_transcript_28764-T1
Valid prediction for GlimmerHMM_glimmerT_5084-T1
Valid prediction for HiQ_model.g3444.t1
Valid prediction for snap_scaffold_2-snap.2976-T1
Valid prediction for snap_scaffold_2-snap.2979-T1
Valid prediction for CodingQuarry_transcript_28772-T1
Valid prediction for snap_scaffold_2-snap.2970-T1
Valid prediction for HiQ_model.g3431.t1
Valid prediction for Augustus_model.g3441.t1
Valid prediction for CodingQuarry_transcript_28769-T1
Couldn't classify 89976, 90138
Couldn't classify 91593, 91813
Sorry, prediction pasa_asmbl_25431.p1 fails validation.
(CCT)	 AT	89976-90138	GT	AGG
(GTC)	 AG	91593-91813	GC	TGG
-recovered pasa_asmbl_25431.p1, internal, 91593, 91813
Valid prediction for GlimmerHMM_glimmerT_5078-T1
Valid prediction for HiQ_model.g3429.t1
Valid prediction for snap_scaffold_2-snap.2963-T1
Valid prediction for GlimmerHMM_glimmerT_5094-T1
Valid prediction for GlimmerHMM_glimmerT_5087-T1
Valid prediction for Augustus_model.g3437.t1
Valid prediction for CodingQuarry_transcript_28770-T1
Valid prediction for snap_scaffold_2-snap.2983-T1
Valid prediction for GlimmerHMM_glimmerT_5092-T1
Valid prediction for pasa_asmbl_25056.p1
Valid prediction for GlimmerHMM_glimmerT_5073-T1
Valid prediction for Augustus_model.g3446.t1
Valid prediction for GlimmerHMM_glimmerT_5062-T1
Valid prediction for GlimmerHMM_glimmerT_5089-T1
Valid prediction for GlimmerHMM_glimmerT_5080-T1
Valid prediction for GlimmerHMM_glimmerT_5070-T1
Valid prediction for CodingQuarry_transcript_28775-T1
Couldn't classify 194777, 194832
Couldn't classify 195841, 196234
Sorry, prediction pasa_asmbl_25062.p1 fails validation.
(GAG)	 GC	194777-194832	GT	AGG
(TCA)	 AG	195018-195176	GT	AGG
(ATC)	 AG	195397-195729	GT	AGG
(GTC)	 AG	195841-196234	GG	GGG
-recovered pasa_asmbl_25062.p1, internal, 195018, 195176
-recovered pasa_asmbl_25062.p1, internal, 195397, 195729
Valid prediction for Augustus_model.g3438.t1
Valid prediction for CodingQuarry_transcript_28765-T1
Valid prediction for CodingQuarry_transcript_28766-T1
Valid prediction for snap_scaffold_2-snap.2961-T1
Valid prediction for snap_scaffold_2-snap.2966-T1
Valid prediction for snap_scaffold_2-snap.2982-T1
Valid prediction for Augustus_model.g3433.t1
Valid prediction for Augustus_model.g3419.t1
Valid prediction for Augustus_model.g3430.t1
Valid prediction for snap_scaffold_2-snap.2952-T1
Valid prediction for GlimmerHMM_glimmerT_5071-T1
Valid prediction for snap_scaffold_2-snap.2969-T1
Couldn't classify 27374, 27418
Sorry, prediction pasa_asmbl_25037.p2 fails validation.
(CTA)	 TA	27374-27418	GT	TGG
(CGG)	 AG	27762-27833	GT	TAG
(TCA)	 AG	27919-27984	GT	ATG
(TAT)	 AG	28066-28105	GT	TGG
(AAA)	 AG	28184-28303	GT	AGG
(AGC)	 AG	28393-28473	GT	ACG
(TTG)	 AG	28551-28727	GT	AGG
(AGT)	 AG	28837-28877	AG	GAA
-recovered pasa_asmbl_25037.p2, terminal, 28837, 28877
-recovered pasa_asmbl_25037.p2, internal, 27762, 27833
-recovered pasa_asmbl_25037.p2, internal, 27919, 27984
-recovered pasa_asmbl_25037.p2, internal, 28066, 28105
-recovered pasa_asmbl_25037.p2, internal, 28184, 28303
-recovered pasa_asmbl_25037.p2, internal, 28393, 28473
-recovered pasa_asmbl_25037.p2, internal, 28551, 28727
Valid prediction for pasa_asmbl_25065.p1
Valid prediction for snap_scaffold_2-snap.2984-T1
Couldn't classify 59125, 59188
Sorry, prediction pasa_asmbl_25046.p2 fails validation.
(CCA)	 AG	59125-59188	GT	TGG
(GCA)	 AG	59266-59341	GT	TAG
(CCA)	 AG	59672-59846	GT	CTG
(GGC)	 AG	60618-60746	GC	AAG
-recovered pasa_asmbl_25046.p2, terminal, 60618, 60746
-recovered pasa_asmbl_25046.p2, internal, 59125, 59188
-recovered pasa_asmbl_25046.p2, internal, 59266, 59341
-recovered pasa_asmbl_25046.p2, internal, 59672, 59846
-recovered pasa_asmbl_25046.p2, internal, 60618, 60746
Valid prediction for GlimmerHMM_glimmerT_5104-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_2-snap.2954-T1
Valid prediction for Augustus_model.g3424.t1
Valid prediction for CodingQuarry_transcript_28774-T1
Couldn't classify 4040, 4267
Couldn't classify 6514, 6567
Sorry, prediction pasa_asmbl_23652.p1 fails validation.
(GAG)	 AG	4040-4267	GT	TGG
(TGG)	 AG	4367-4436	GT	AGG
(GTC)	 AG	4530-4699	GT	AGG
(GTC)	 AG	5480-5718	GT	AAG
(GCA)	 AG	5825-5891	GT	AGG
(CTG)	 AG	6062-6120	GT	AGG
(TGG)	 AG	6244-6388	GT	CGG
(ATG)	 AG	6514-6567	CT	CCC
-recovered pasa_asmbl_23652.p1, internal, 4040, 4267
-recovered pasa_asmbl_23652.p1, internal, 4367, 4436
-recovered pasa_asmbl_23652.p1, internal, 4530, 4699
-recovered pasa_asmbl_23652.p1, internal, 5480, 5718
-recovered pasa_asmbl_23652.p1, internal, 5825, 5891
-recovered pasa_asmbl_23652.p1, internal, 6062, 6120
-recovered pasa_asmbl_23652.p1, internal, 6244, 6388
Valid prediction for CodingQuarry_transcript_28763-T1
Valid prediction for Augustus_model.g3425.t1
Valid prediction for Augustus_model.g3420.t1
Valid prediction for GlimmerHMM_glimmerT_5101-T1
Valid prediction for CodingQuarry_transcript_28767-T1
Valid prediction for pasa_asmbl_23650.p1
Valid prediction for GlimmerHMM_glimmerT_5105-T1
Valid prediction for snap_scaffold_2-snap.2989-T1
Valid prediction for GlimmerHMM_glimmerT_5106-T1
Couldn't classify 227168, 227195
Couldn't classify 228161, 228188
Sorry, prediction pasa_asmbl_23628.p1 fails validation.
(GTA)	 TG	227168-227195	GT	AGG
(ATA)	 AG	227285-227440	GT	AGG
(CCC)	 AG	227587-227669	GT	AGG
(GAC)	 AG	227760-227854	GT	AGG
(AGA)	 AG	227948-228052	GT	AGG
(GAA)	 AG	228161-228188	AT	CTA
add_exon() Sorry, pasa_asmbl_23628.p1 227285-227440-terminal-1 is invalid.
-recovered pasa_asmbl_23628.p1, terminal, 227285, 227440
-recovered pasa_asmbl_23628.p1, internal, 227285, 227440
-recovered pasa_asmbl_23628.p1, internal, 227587, 227669
-recovered pasa_asmbl_23628.p1, internal, 227760, 227854
-recovered pasa_asmbl_23628.p1, internal, 227948, 228052
Valid prediction for snap_scaffold_2-snap.2959-T1
Valid prediction for GlimmerHMM_glimmerT_5083-T1
Valid prediction for GlimmerHMM_glimmerT_5074-T1
Couldn't classify 3493, 3798
Sorry, prediction pasa_asmbl_23653.p1 fails validation.
(ATG)	 AC	3493-3798	CT	ATC
Valid prediction for GlimmerHMM_glimmerT_5085-T1
Valid prediction for CodingQuarry_transcript_28773-T1
Valid prediction for snap_scaffold_2-snap.2993-T1
Valid prediction for pasa_asmbl_23648.p1
Couldn't classify 228246, 228317
Sorry, prediction pasa_asmbl_23626.p1 fails validation.
(AGT)	 TC	228246-228317	GT	AGG
(GTA)	 AG	228449-228592	GT	AGG
(GTT)	 AG	228717-228826	GT	CTG
(GCT)	 AG	228936-229015	GT	TGG
(GTT)	 AG	229097-229239	GT	AGG
(GCT)	 AG	229319-229422	GT	TAG
(CTG)	 AG	229569-229680	AT	AAA
-recovered pasa_asmbl_23626.p1, terminal, 229569, 229680
-recovered pasa_asmbl_23626.p1, internal, 228449, 228592
-recovered pasa_asmbl_23626.p1, internal, 228717, 228826
-recovered pasa_asmbl_23626.p1, internal, 228936, 229015
-recovered pasa_asmbl_23626.p1, internal, 229097, 229239
-recovered pasa_asmbl_23626.p1, internal, 229319, 229422
Valid prediction for snap_scaffold_2-snap.2978-T1
Valid prediction for GlimmerHMM_glimmerT_5076-T1
Valid prediction for HiQ_model.g3447.t1
Valid prediction for snap_scaffold_2-snap.2986-T1
Couldn't classify 49300, 49728
Sorry, prediction pasa_asmbl_23641.p1 fails validation.
(TCT)	 TG	49300-49728	AA	GAA
Valid prediction for GlimmerHMM_glimmerT_5067-T1
Valid prediction for snap_scaffold_2-snap.2965-T1
Valid prediction for snap_scaffold_2-snap.2953-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.2987-T1
Valid prediction for GlimmerHMM_glimmerT_5081-T1
Valid prediction for GlimmerHMM_glimmerT_5063-T1
Valid prediction for GlimmerHMM_glimmerT_5075-T1
Valid prediction for Augustus_model.g3442.t1
Valid prediction for CodingQuarry_transcript_28776-T1
Valid prediction for GlimmerHMM_glimmerT_5077-T1
Valid prediction for pasa_asmbl_23640.p1
Valid prediction for snap_scaffold_2-snap.2992-T1
Valid prediction for GlimmerHMM_glimmerT_5090-T1
Valid prediction for GlimmerHMM_glimmerT_5086-T1
Valid prediction for CodingQuarry_transcript_28777-T1
Valid prediction for GlimmerHMM_glimmerT_5082-T1
Valid prediction for snap_scaffold_2-snap.2958-T1
Valid prediction for Augustus_model.g3440.t1
Valid prediction for snap_scaffold_2-snap.2985-T1
Couldn't classify 225864, 225881
Couldn't classify 226897, 226980
Sorry, prediction pasa_asmbl_23630.p1 fails validation.
(CTT)	 AC	225864-225881	GT	CTG
(CAC)	 AG	226032-226127	GT	ATG
(CTG)	 AG	226269-226414	GT	AAG
(GGT)	 AG	226658-226781	GT	AGG
(ATC)	 AG	226897-226980	TT	CGT
-recovered pasa_asmbl_23630.p1, internal, 226032, 226127
-recovered pasa_asmbl_23630.p1, internal, 226269, 226414
-recovered pasa_asmbl_23630.p1, internal, 226658, 226781
Couldn't classify 46777, 47047
Sorry, prediction pasa_asmbl_23643.p3 fails validation.
(GTG)	 AC	46777-47047	GT	GGG
(AAT)	 AG	47638-47675	GT	AGG
(GTG)	 AG	48587-48592	AG	AAA
-recovered pasa_asmbl_23643.p3, terminal, 48587, 48592
-recovered pasa_asmbl_23643.p3, internal, 47638, 47675
Valid prediction for HiQ_model.g3443.t1
Valid prediction for GlimmerHMM_glimmerT_5098-T1
Valid prediction for GlimmerHMM_glimmerT_5095-T1
Valid prediction for HiQ_model.g3445.t1
Valid prediction for snap_scaffold_2-snap.2977-T1
Valid prediction for snap_scaffold_2-snap.2967-T1
Valid prediction for Augustus_model.g3426.t1
Valid prediction for snap_scaffold_2-snap.2974-T1
Valid prediction for pasa_asmbl_23625.p1
Valid prediction for snap_scaffold_2-snap.2981-T1
Valid prediction for snap_scaffold_2-snap.2972-T1
Valid prediction for GlimmerHMM_glimmerT_5064-T1
Valid prediction for GlimmerHMM_glimmerT_5079-T1
Valid prediction for CodingQuarry_transcript_28768-T1
Valid prediction for snap_scaffold_2-snap.2964-T1
Valid prediction for GlimmerHMM_glimmerT_5102-T1
Valid prediction for snap_scaffold_2-snap.2973-T1
Valid prediction for snap_scaffold_2-snap.2957-T1
Valid prediction for pasa_asmbl_23645.p1
Valid prediction for Augustus_model.g3436.t1
Valid prediction for Augustus_model.g3434.t1
Valid prediction for GlimmerHMM_glimmerT_5096-T1
Valid prediction for snap_scaffold_2-snap.2971-T1
Valid prediction for pasa_asmbl_23632.p1
Valid prediction for GlimmerHMM_glimmerT_5093-T1
Valid prediction for Augustus_model.g3439.t1
Valid prediction for GlimmerHMM_glimmerT_5103-T1
Valid prediction for GlimmerHMM_glimmerT_5066-T1
Valid prediction for Augustus_model.g3435.t1
Valid prediction for Augustus_model.g3432.t1
Valid prediction for GlimmerHMM_glimmerT_5072-T1
Valid prediction for HiQ_model.g3421.t1
Valid prediction for GlimmerHMM_glimmerT_5088-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 91812, rend_intergenic: 89481  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103654, rend_intergenic: 99399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147438, rend_intergenic: 112078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152124, rend_intergenic: 149250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165646, rend_intergenic: 152226  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185178, rend_intergenic: 167088  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198834, rend_intergenic: 185979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 262683
-exon list size: 625


building trellis

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55.3    
55.5    
55.7    
55.8    
56.0    
56.1    
56.3    
56.5    
56.6    
56.8    
56.9    
57.1    
57.3    
57.4    
57.6    
57.7    
57.9    
58.1    
58.2    
58.4    
58.5    
58.7    
58.9    
59.0    
59.2    
59.3    
59.5    
59.6    
59.8    
60.0    
60.1    
60.3    
60.4    
60.6    
60.8    
60.9    
61.1    
61.2    
61.4    
61.6    
61.7    
61.9    
62.0    
62.2    
62.4    
62.5    
62.7    
62.8    
63.0    
63.2    
63.3    
63.5    
63.6    
63.8    
64.0    
64.1    
64.3    
64.4    
64.6    
64.8    
64.9    
65.1    
65.2    
65.4    
65.6    
65.7    
65.9    
66.0    
66.2    
66.3    
66.5    
66.7    
66.8    
67.0    
67.1    
67.3    
67.5    
67.6    
67.8    
67.9    
68.1    
68.3    
68.4    
68.6    
68.7    
68.9    
69.1    
69.2    
69.4    
69.5    
69.7    
69.9    
70.0    
70.2    
70.3    
70.5    
70.7    
70.8    
71.0    
71.1    
71.3    
71.5    
71.6    
71.8    
71.9    
72.1    
72.2    
72.4    
72.6    
72.7    
72.9    
73.0    
73.2    
73.4    
73.5    
73.7    
73.8    
74.0    
74.2    
74.3    
74.5    
74.6    
74.8    
75.0    
75.1    
75.3    
75.4    
75.6    
75.8    
75.9    
76.1    
76.2    
76.4    
76.6    
76.7    
76.9    
77.0    
77.2    
77.4    
77.5    
77.7    
77.8    
78.0    
78.1    
78.3    
78.5    
78.6    
78.8    
78.9    
79.1    
79.3    
79.4    
79.6    
79.7    
79.9    
80.1    
80.2    
80.4    
80.5    
80.7    
80.9    
81.0    
81.2    
81.3    
81.5    
81.7    
81.8    
82.0    
82.1    
82.3    
82.5    
82.6    
82.8    
82.9    
83.1    
83.3    
83.4    
83.6    
83.7    
83.9    
84.1    
84.2    
84.4    
84.5    
84.7    
84.8    
85.0    
85.2    
85.3    
85.5    
85.6    
85.8    
86.0    
86.1    
86.3    
86.4    
86.6    
86.8    
86.9    
87.1    
87.2    
87.4    
87.6    
87.7    
87.9    
88.0    
88.2    
88.4    
88.5    
88.7    
88.8    
89.0    
89.2    
89.3    
89.5    
89.6    
89.8    
90.0    
90.1    
90.3    
90.4    
90.6    
90.7    
90.9    
91.1    
91.2    
91.4    
91.5    
91.7    
91.9    
92.0    
92.2    
92.3    
92.5    
92.7    
92.8    
93.0    
93.1    
93.3    
93.5    
93.6    
93.8    
93.9    
94.1    
94.3    
94.4    
94.6    
94.7    
94.9    
95.1    
95.2    
95.4    
95.5    
95.7    
95.9    
96.0    
96.2    
96.3    
96.5    
96.7    
96.8    
97.0    
97.1    
97.3    
97.4    
97.6    
97.8    
97.9    
98.1    
98.2    
98.4    
98.6    
98.7    
98.9    
99.0    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 91812, rend_intergenic: 89481  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103654, rend_intergenic: 99399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147438, rend_intergenic: 112078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152124, rend_intergenic: 149250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165646, rend_intergenic: 152226  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185178, rend_intergenic: 167088  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198834, rend_intergenic: 185979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support