-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_20/scaffold_20_9060578-9228805

-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_46564-T1
Valid prediction for snap_scaffold_20-snap.1975-T1
Couldn't classify 23783, 23977
Couldn't classify 28323, 28427
Sorry, prediction pasa_asmbl_26820.p1 fails validation.
(AGC)	 AG	23783-23977	GT	AGG
(GTC)	 AG	24342-24450	GT	AGG
(ATG)	 AG	24612-24760	GT	AGG
(GAC)	 AG	25168-25288	GT	GGG
(GTA)	 AG	27965-28110	GT	AGG
(GCC)	 AG	28323-28427	AT	TCA
add_exon() Sorry, pasa_asmbl_26820.p1 24612-24760-initial-1 is invalid.
-recovered pasa_asmbl_26820.p1, initial, 24612, 24760
-recovered pasa_asmbl_26820.p1, internal, 23783, 23977
-recovered pasa_asmbl_26820.p1, internal, 24342, 24450
-recovered pasa_asmbl_26820.p1, internal, 24612, 24760
-recovered pasa_asmbl_26820.p1, internal, 25168, 25288
-recovered pasa_asmbl_26820.p1, internal, 27965, 28110
Valid prediction for Augustus_model.g30939.t1
Couldn't classify 110403, 110534
Couldn't classify 111624, 111756
Sorry, prediction pasa_asmbl_26838.p1 fails validation.
(GAG)	 TG	110403-110534	GT	AGG
(GAG)	 AG	110638-110761	GT	GGG
(ACC)	 AG	110914-111085	GT	AGG
(GAT)	 AG	111244-111456	GT	AGG
(GGC)	 AG	111624-111756	CA	AGC
-recovered pasa_asmbl_26838.p1, internal, 110638, 110761
-recovered pasa_asmbl_26838.p1, internal, 110914, 111085
-recovered pasa_asmbl_26838.p1, internal, 111244, 111456
Valid prediction for Augustus_model.g30937.t1
Valid prediction for Augustus_model.g30935.t1
Valid prediction for Augustus_model.g30940.t1
Valid prediction for GlimmerHMM_glimmerT_46570-T1
Valid prediction for GlimmerHMM_glimmerT_46574-T1
Valid prediction for GlimmerHMM_glimmerT_46562-T1
Valid prediction for Augustus_model.g30941.t1
Valid prediction for GlimmerHMM_glimmerT_46575-T1
Valid prediction for HiQ_model.g30923.t1
Couldn't classify 115156, 115367
Sorry, prediction pasa_asmbl_26839.p1 fails validation.
(CAG)	 GA	115156-115367	GT	AAG
(GGA)	 AG	115655-115763	GT	AGG
(GCG)	 AG	115899-116071	GT	AGG
(ACG)	 AG	116319-116427	AC	GAA
-recovered pasa_asmbl_26839.p1, terminal, 116319, 116427
-recovered pasa_asmbl_26839.p1, internal, 115655, 115763
-recovered pasa_asmbl_26839.p1, internal, 115899, 116071
Valid prediction for Augustus_model.g30938.t1
Valid prediction for snap_scaffold_20-snap.2002-T1
Valid prediction for GlimmerHMM_glimmerT_46559-T1
Valid prediction for snap_scaffold_20-snap.1980-T1
Valid prediction for Augustus_model.g30930.t1
Valid prediction for snap_scaffold_20-snap.1991-T1
Valid prediction for pasa_asmbl_26835.p1
Valid prediction for CodingQuarry_transcript_30588-T1
Valid prediction for snap_scaffold_20-snap.1998-T1
Valid prediction for CodingQuarry_transcript_30590-T1
Valid prediction for CodingQuarry_transcript_30589-T1
Valid prediction for Augustus_model.g30931.t1
Valid prediction for GlimmerHMM_glimmerT_46577-T1
Valid prediction for GlimmerHMM_glimmerT_46565-T1
Valid prediction for snap_scaffold_20-snap.2004-T1
Valid prediction for snap_scaffold_20-snap.1994-T1
Valid prediction for snap_scaffold_20-snap.1987-T1
Valid prediction for GlimmerHMM_glimmerT_46567-T1
Valid prediction for GlimmerHMM_glimmerT_46573-T1
Valid prediction for GlimmerHMM_glimmerT_46582-T1
Valid prediction for HiQ_model.g30924.t1
Valid prediction for GlimmerHMM_glimmerT_46571-T1
Valid prediction for snap_scaffold_20-snap.2007-T1
Valid prediction for snap_scaffold_20-snap.1974-T1
Couldn't classify 33379, 33438
Sorry, prediction pasa_asmbl_26822.p1 fails validation.
(CCT)	 CG	33379-33438	GT	AGG
(GTG)	 AG	33607-33698	GT	AGG
(TCT)	 AG	33981-34157	GT	ATG
(TTT)	 AG	34489-34551	GT	CGG
(GGA)	 AG	34711-34787	GC	AGG
(GGA)	 AG	35111-35253	GT	AGG
(TCT)	 AG	35583-35690	GT	GGG
(CTG)	 AG	35794-35874	GT	GGG
(GGT)	 AG	36179-36382	GG	AGG
-recovered pasa_asmbl_26822.p1, terminal, 36179, 36382
-recovered pasa_asmbl_26822.p1, internal, 33607, 33698
-recovered pasa_asmbl_26822.p1, internal, 33981, 34157
-recovered pasa_asmbl_26822.p1, internal, 34489, 34551
-recovered pasa_asmbl_26822.p1, internal, 34711, 34787
-recovered pasa_asmbl_26822.p1, internal, 35111, 35253
-recovered pasa_asmbl_26822.p1, internal, 35583, 35690
-recovered pasa_asmbl_26822.p1, internal, 35794, 35874
Valid prediction for snap_scaffold_20-snap.2006-T1
Couldn't classify 124449, 124496
Sorry, prediction pasa_asmbl_26840.p1 fails validation.
(CTA)	 CT	124449-124496	GT	AGG
(AAG)	 AG	124771-124899	GT	AGG
(GCT)	 AG	125066-125113	GT	ATG
(GAA)	 AG	125221-125298	TG	AAT
-recovered pasa_asmbl_26840.p1, terminal, 125221, 125298
-recovered pasa_asmbl_26840.p1, internal, 124771, 124899
-recovered pasa_asmbl_26840.p1, internal, 125066, 125113
Valid prediction for Augustus_model.g30922.t1
Valid prediction for GlimmerHMM_glimmerT_46563-T1
Valid prediction for pasa_asmbl_26836.p1
Valid prediction for snap_scaffold_20-snap.1988-T1
Valid prediction for HiQ_model.g30927.t1
Couldn't classify 29039, 29114
Couldn't classify 33144, 33179
Sorry, prediction pasa_asmbl_26821.p1 fails validation.
(CGC)	 TG	29039-29114	GT	CAG
(CGG)	 AG	30128-30237	GT	GGG
(TTC)	 AG	30678-30821	GT	AGG
(GTT)	 AG	31322-31397	GT	AGG
(GTA)	 AG	31652-31787	GT	GGG
(GGA)	 AG	32463-32544	GT	CGG
(GAT)	 AG	33144-33179	GA	CAG
-recovered pasa_asmbl_26821.p1, internal, 30128, 30237
-recovered pasa_asmbl_26821.p1, internal, 30678, 30821
-recovered pasa_asmbl_26821.p1, internal, 31322, 31397
-recovered pasa_asmbl_26821.p1, internal, 31652, 31787
-recovered pasa_asmbl_26821.p1, internal, 32463, 32544
Valid prediction for snap_scaffold_20-snap.1993-T1
Valid prediction for snap_scaffold_20-snap.2001-T1
Valid prediction for snap_scaffold_20-snap.1995-T1
Valid prediction for GlimmerHMM_glimmerT_46580-T1
Valid prediction for snap_scaffold_20-snap.1978-T1
Valid prediction for snap_scaffold_20-snap.1984-T1
Couldn't classify 38603, 38699
Couldn't classify 47806, 47917
Sorry, prediction pasa_asmbl_26825.p1 fails validation.
(CGA)	 CC	38603-38699	GT	AAG
(TCA)	 AG	40356-40403	GT	AGG
(CTC)	 AG	42358-42502	GT	AAG
(CGC)	 AG	42928-42994	GT	AGG
(AGA)	 AG	43568-43681	GT	AGG
(CAA)	 AG	44255-44374	GT	ATG
(ACG)	 AG	44476-44583	GT	CGG
(ATC)	 AG	44835-45014	GT	CGG
(CCT)	 AG	45223-45303	GT	TGG
(GTG)	 AG	45500-45642	GT	TGG
(CCT)	 AG	45771-45816	GT	TAG
(GAG)	 AG	45936-46075	GT	AGG
(CTC)	 AG	47806-47917	CT	CCC
-recovered pasa_asmbl_26825.p1, internal, 40356, 40403
-recovered pasa_asmbl_26825.p1, internal, 42358, 42502
-recovered pasa_asmbl_26825.p1, internal, 42928, 42994
-recovered pasa_asmbl_26825.p1, internal, 43568, 43681
-recovered pasa_asmbl_26825.p1, internal, 44255, 44374
-recovered pasa_asmbl_26825.p1, internal, 44476, 44583
-recovered pasa_asmbl_26825.p1, internal, 44835, 45014
-recovered pasa_asmbl_26825.p1, internal, 45223, 45303
-recovered pasa_asmbl_26825.p1, internal, 45500, 45642
-recovered pasa_asmbl_26825.p1, internal, 45771, 45816
-recovered pasa_asmbl_26825.p1, internal, 45936, 46075
Valid prediction for GlimmerHMM_glimmerT_46578-T1
Valid prediction for snap_scaffold_20-snap.2008-T1
Valid prediction for HiQ_model.g30933.t1
Valid prediction for GlimmerHMM_glimmerT_46581-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 Augustus_model.g30925.t1
Valid prediction for snap_scaffold_20-snap.2009-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_20-snap.1996-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_46560-T1
Valid prediction for HiQ_model.g30928.t1
Valid prediction for snap_scaffold_20-snap.1981-T1
Couldn't classify 131403, 131747
Sorry, prediction pasa_asmbl_26823.p1 fails validation.
(GGT)	 GG	131403-131747	AA	AAA
Valid prediction for snap_scaffold_20-snap.1990-T1
Valid prediction for GlimmerHMM_glimmerT_46572-T1
Valid prediction for Augustus_model.g30921.t1
Valid prediction for GlimmerHMM_glimmerT_46569-T1
Valid prediction for snap_scaffold_20-snap.1986-T1
Valid prediction for Augustus_model.g30929.t1
Valid prediction for HiQ_model.g30932.t1
Couldn't classify 45100, 45229
Sorry, prediction pasa_asmbl_26269.p1 fails validation.
(ATG)	 AA	44199-44294	GT	AGG
(GAG)	 AG	44585-44751	GT	GAG
(GTG)	 AG	45100-45229	CC	AGC
-recovered pasa_asmbl_26269.p1, initial, 44199, 44294
-recovered pasa_asmbl_26269.p1, internal, 44585, 44751
Valid prediction for snap_scaffold_20-snap.2000-T1
Valid prediction for GlimmerHMM_glimmerT_46568-T1
Valid prediction for Augustus_model.g30934.t1
Valid prediction for pasa_asmbl_26020.p1
Valid prediction for GlimmerHMM_glimmerT_46576-T1
Valid prediction for Augustus_model.g30920.t1
Valid prediction for snap_scaffold_20-snap.1976-T1
Valid prediction for GlimmerHMM_glimmerT_46557-T1
Valid prediction for CodingQuarry_transcript_30591-T1
Valid prediction for snap_scaffold_20-snap.1979-T1
Valid prediction for snap_scaffold_20-snap.1982-T1
Valid prediction for snap_scaffold_20-snap.1977-T1
Valid prediction for snap_scaffold_20-snap.1989-T1
Valid prediction for CodingQuarry_transcript_30592-T1
Valid prediction for GlimmerHMM_glimmerT_46561-T1
Valid prediction for snap_scaffold_20-snap.2003-T1
Valid prediction for snap_scaffold_20-snap.1985-T1
Valid prediction for snap_scaffold_20-snap.2005-T1
Valid prediction for snap_scaffold_20-snap.1997-T1
Couldn't classify 103203, 103324
Sorry, prediction Augustus_model.g30926.t1 fails validation.
(ATG)	 GA	91988-92014	GT	AGG
(GTG)	 AG	92259-92335	GT	AGG
(CGG)	 AG	92437-92643	GT	AGG
(GCT)	 AG	93582-93771	GT	AGG
(GAG)	 AG	94110-94334	GT	AGG
(GCA)	 AG	94602-94676	GT	AAG
(ATG)	 AG	94792-94917	GT	AGG
(GAG)	 AG	95464-95607	GT	AGG
(GGT)	 AG	95928-96017	GT	AGG
(CAC)	 AG	96139-96236	GT	AAG
(GCT)	 AG	96495-96555	GT	AGG
(GAG)	 AG	97188-97220	GT	AGG
(GGT)	 AG	97871-98011	GT	AGG
(TAC)	 AG	100174-100272	GT	AGG
(AGG)	 AG	100503-100643	GT	AGG
(GAA)	 AG	100814-100939	GT	AGG
(AAC)	 AG	101122-101268	GT	AGG
(AGC)	 AG	101778-101873	GT	AGG
(AAA)	 AG	101961-102056	GT	AGG
(GTC)	 AG	103203-103324	CG	TCC
-recovered Augustus_model.g30926.t1, initial, 91988, 92014
-recovered Augustus_model.g30926.t1, initial, 94792, 94917
-recovered Augustus_model.g30926.t1, internal, 92259, 92335
-recovered Augustus_model.g30926.t1, internal, 92437, 92643
-recovered Augustus_model.g30926.t1, internal, 93582, 93771
-recovered Augustus_model.g30926.t1, internal, 94110, 94334
-recovered Augustus_model.g30926.t1, internal, 94602, 94676
-recovered Augustus_model.g30926.t1, internal, 94792, 94917
-recovered Augustus_model.g30926.t1, internal, 95464, 95607
-recovered Augustus_model.g30926.t1, internal, 95928, 96017
-recovered Augustus_model.g30926.t1, internal, 96139, 96236
-recovered Augustus_model.g30926.t1, internal, 96495, 96555
-recovered Augustus_model.g30926.t1, internal, 97188, 97220
-recovered Augustus_model.g30926.t1, internal, 97871, 98011
-recovered Augustus_model.g30926.t1, internal, 100174, 100272
-recovered Augustus_model.g30926.t1, internal, 100503, 100643
-recovered Augustus_model.g30926.t1, internal, 100814, 100939
-recovered Augustus_model.g30926.t1, internal, 101122, 101268
-recovered Augustus_model.g30926.t1, internal, 101778, 101873
-recovered Augustus_model.g30926.t1, internal, 101961, 102056
Valid prediction for snap_scaffold_20-snap.1999-T1
Valid prediction for GlimmerHMM_glimmerT_46579-T1
Valid prediction for snap_scaffold_20-snap.1983-T1
Valid prediction for snap_scaffold_20-snap.1992-T1
Valid prediction for snap_scaffold_20-snap.1973-T1
Valid prediction for Augustus_model.g30936.t1
Valid prediction for GlimmerHMM_glimmerT_46558-T1
Valid prediction for Augustus_model.g30919.t1
Valid prediction for GlimmerHMM_glimmerT_46566-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 36382, rend_intergenic: 13299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48351, rend_intergenic: 44422  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58300, rend_intergenic: 55615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67448, rend_intergenic: 65219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79094, rend_intergenic: 76786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120160, rend_intergenic: 118461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139474, rend_intergenic: 133365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139949, rend_intergenic: 139600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149451, rend_intergenic: 145155  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165577, rend_intergenic: 162098  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 10059, rend_intergenic: 10056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 168228
-exon list size: 443


building trellis

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89.0    
89.2    
89.4    
89.7    
89.9    
90.1    
90.3    
90.6    
90.8    
91.0    
91.2    
91.5    
91.7    
91.9    
92.1    
92.4    
92.6    
92.8    
93.0    
93.3    
93.5    
93.7    
93.9    
94.2    
94.4    
94.6    
94.8    
95.1    
95.3    
95.5    
95.7    
96.0    
96.2    
96.4    
96.6    
96.9    
97.1    
97.3    
97.5    
97.8    
98.0    
98.2    
98.4    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 36382, rend_intergenic: 13299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48351, rend_intergenic: 44422  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58300, rend_intergenic: 55615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67448, rend_intergenic: 65219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79094, rend_intergenic: 76786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120160, rend_intergenic: 118461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139474, rend_intergenic: 133365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139949, rend_intergenic: 139600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149451, rend_intergenic: 145155  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165577, rend_intergenic: 162098  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 10059, rend_intergenic: 10056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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