-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_25/scaffold_25_9112615-9284812

-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_25-snap.1988-T1
Valid prediction for snap_scaffold_25-snap.1992-T1
Valid prediction for GlimmerHMM_glimmerT_54759-T1
Valid prediction for HiQ_model.g36344.t1
Valid prediction for HiQ_model.g36345.t1
Valid prediction for Augustus_model.g36333.t1
Valid prediction for snap_scaffold_25-snap.1996-T1
Valid prediction for CodingQuarry_transcript_38828-T1
Valid prediction for snap_scaffold_25-snap.1980-T1
Valid prediction for pasa_asmbl_33798.p1
Valid prediction for GlimmerHMM_glimmerT_54760-T1
Valid prediction for snap_scaffold_25-snap.1986-T1
Valid prediction for Augustus_model.g36346.t1
Valid prediction for CodingQuarry_transcript_38830-T1
Couldn't classify 51571, 52078
Sorry, prediction pasa_asmbl_33788.p1 fails validation.
(CGG)	 AA	51571-52078	GT	AGG
(AGC)	 AG	52305-52474	GT	AAG
(GGA)	 AG	52799-52927	GT	AGG
(TGT)	 AG	53375-53485	AC	AGA
-recovered pasa_asmbl_33788.p1, terminal, 53375, 53485
-recovered pasa_asmbl_33788.p1, internal, 52305, 52474
-recovered pasa_asmbl_33788.p1, internal, 52799, 52927
Couldn't classify 142746, 142753
Couldn't classify 144355, 144436
Sorry, prediction pasa_asmbl_33795.p1 fails validation.
(CTG)	 AG	142746-142753	GT	AAG
(CAA)	 AG	142870-142986	GT	AAG
(GCT)	 AG	143104-143298	GT	AGG
(GAA)	 AG	144355-144436	CT	CCC
-recovered pasa_asmbl_33795.p1, internal, 142746, 142753
-recovered pasa_asmbl_33795.p1, internal, 142870, 142986
-recovered pasa_asmbl_33795.p1, internal, 143104, 143298
Valid prediction for GlimmerHMM_glimmerT_54764-T1
Valid prediction for snap_scaffold_25-snap.2004-T1
Valid prediction for GlimmerHMM_glimmerT_54773-T1
Valid prediction for CodingQuarry_transcript_38831-T1
Couldn't classify 130201, 131130
Sorry, prediction pasa_asmbl_33792.p1 fails validation.
(ATG)	 AG	130201-131130	AG	AGA
Valid prediction for GlimmerHMM_glimmerT_54776-T1
Valid prediction for pasa_asmbl_33783.p1
Valid prediction for GlimmerHMM_glimmerT_54762-T1
Valid prediction for snap_scaffold_25-snap.1978-T1
Valid prediction for snap_scaffold_25-snap.2001-T1
Valid prediction for HiQ_model.g36334.t1
Valid prediction for GlimmerHMM_glimmerT_54779-T1
Valid prediction for GlimmerHMM_glimmerT_54765-T1
Valid prediction for snap_scaffold_25-snap.2011-T1
Valid prediction for snap_scaffold_25-snap.1973-T1
Valid prediction for snap_scaffold_25-snap.1977-T1
Valid prediction for HiQ_model.g36331.t1
Valid prediction for Augustus_model.g36338.t1
Valid prediction for GlimmerHMM_glimmerT_54770-T1
Valid prediction for GlimmerHMM_glimmerT_54768-T1
Valid prediction for snap_scaffold_25-snap.1999-T1
Valid prediction for pasa_asmbl_33799.p1
Valid prediction for snap_scaffold_25-snap.1998-T1
Valid prediction for Augustus_model.g36342.t1
Valid prediction for GlimmerHMM_glimmerT_54778-T1
Valid prediction for GlimmerHMM_glimmerT_54763-T1
Valid prediction for GlimmerHMM_glimmerT_54771-T1
Valid prediction for snap_scaffold_25-snap.2010-T1
Valid prediction for snap_scaffold_25-snap.1989-T1
Couldn't classify 145271, 146164
Sorry, prediction pasa_asmbl_33797.p1 fails validation.
(CCA)	 CC	145271-146164	CT	GAC
Couldn't classify 139576, 139802
Couldn't classify 142623, 142646
Sorry, prediction pasa_asmbl_33793.p1 fails validation.
(CTC)	 GC	139576-139802	GT	AGG
(GCT)	 AG	140447-140649	GT	CGG
(AGC)	 AG	140937-140997	GT	AGG
(AAA)	 AG	141107-141202	GT	CGG
(GTT)	 AG	141321-141476	GT	AGG
(CTT)	 AG	141589-141789	GT	AGG
(CAA)	 AG	141912-142074	GT	AGG
(TGT)	 AG	142623-142646	CT	AGC
-recovered pasa_asmbl_33793.p1, internal, 140447, 140649
-recovered pasa_asmbl_33793.p1, internal, 140937, 140997
-recovered pasa_asmbl_33793.p1, internal, 141107, 141202
-recovered pasa_asmbl_33793.p1, internal, 141321, 141476
-recovered pasa_asmbl_33793.p1, internal, 141589, 141789
-recovered pasa_asmbl_33793.p1, internal, 141912, 142074
Valid prediction for snap_scaffold_25-snap.2007-T1
Valid prediction for snap_scaffold_25-snap.1976-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.g36341.t1
Valid prediction for Augustus_model.g36339.t1
Valid prediction for GlimmerHMM_glimmerT_54780-T1
Valid prediction for snap_scaffold_25-snap.1990-T1
Valid prediction for snap_scaffold_25-snap.2014-T1
Valid prediction for snap_scaffold_25-snap.2008-T1
Valid prediction for snap_scaffold_25-snap.2000-T1
Valid prediction for GlimmerHMM_glimmerT_54758-T1
Valid prediction for Augustus_model.g36337.t1
Valid prediction for GlimmerHMM_glimmerT_54774-T1
Valid prediction for Augustus_model.g36335.t1
Valid prediction for Augustus_model.g36336.t1
Couldn't classify 71311, 71459
Sorry, prediction pasa_asmbl_34550.p1 fails validation.
(GGC)	 GT	71311-71459	GT	AAG
(GCT)	 AG	71823-71891	GT	AGG
(GTG)	 AG	72036-72065	GT	AAG
(GAT)	 AG	72274-72418	GA	AGG
add_exon() Sorry, pasa_asmbl_34550.p1 72036-72065-terminal-1 is invalid.
-recovered pasa_asmbl_34550.p1, terminal, 72036, 72065
-recovered pasa_asmbl_34550.p1, terminal, 72274, 72418
-recovered pasa_asmbl_34550.p1, internal, 71823, 71891
-recovered pasa_asmbl_34550.p1, internal, 72036, 72065
Valid prediction for snap_scaffold_25-snap.1972-T1
Valid prediction for snap_scaffold_25-snap.2005-T1
Valid prediction for snap_scaffold_25-snap.2009-T1
Valid prediction for Augustus_model.g36343.t1
Valid prediction for GlimmerHMM_glimmerT_54777-T1
Valid prediction for snap_scaffold_25-snap.1994-T1
Valid prediction for GlimmerHMM_glimmerT_54772-T1
Valid prediction for snap_scaffold_25-snap.2006-T1
Valid prediction for snap_scaffold_25-snap.1985-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_25-snap.1981-T1
Valid prediction for snap_scaffold_25-snap.2002-T1
Valid prediction for Augustus_model.g36340.t1
Valid prediction for snap_scaffold_25-snap.2012-T1
Valid prediction for GlimmerHMM_glimmerT_54767-T1
Valid prediction for snap_scaffold_25-snap.1987-T1
Valid prediction for snap_scaffold_25-snap.1995-T1
Valid prediction for snap_scaffold_25-snap.1974-T1
Valid prediction for GlimmerHMM_glimmerT_54761-T1
Valid prediction for CodingQuarry_transcript_38829-T1
Valid prediction for snap_scaffold_25-snap.2015-T1
Valid prediction for snap_scaffold_25-snap.1979-T1
Valid prediction for snap_scaffold_25-snap.1983-T1
Valid prediction for snap_scaffold_25-snap.1997-T1
Valid prediction for snap_scaffold_25-snap.1984-T1
Valid prediction for GlimmerHMM_glimmerT_54769-T1
Valid prediction for snap_scaffold_25-snap.2003-T1
Valid prediction for snap_scaffold_25-snap.1991-T1
Valid prediction for GlimmerHMM_glimmerT_54775-T1
Valid prediction for snap_scaffold_25-snap.1993-T1
Valid prediction for GlimmerHMM_glimmerT_54766-T1
Valid prediction for snap_scaffold_25-snap.1975-T1
Valid prediction for Augustus_model.g36332.t1
Valid prediction for snap_scaffold_25-snap.1982-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8885, rend_intergenic: 6106  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14123, rend_intergenic: 11169  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23481, rend_intergenic: 21370  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40535, rend_intergenic: 25671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48103, rend_intergenic: 43820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66852, rend_intergenic: 61744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89013, rend_intergenic: 87743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98624, rend_intergenic: 93606  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103033, rend_intergenic: 99781  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107195, rend_intergenic: 103167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112298, rend_intergenic: 107214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126167, rend_intergenic: 112821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136879, rend_intergenic: 134685  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146164, rend_intergenic: 136896  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157367, rend_intergenic: 153777  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 172198
-exon list size: 365


building trellis

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43.6    
43.9    
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79.3    
79.6    
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83.1    
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84.2    
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86.1    
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88.0    
88.3    
88.6    
88.8    
89.1    
89.4    
89.6    
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90.2    
90.5    
90.7    
91.0    
91.3    
91.6    
91.8    
92.1    
92.4    
92.6    
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93.2    
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93.7    
94.0    
94.3    
94.6    
94.8    
95.1    
95.4    
95.6    
95.9    
96.2    
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97.0    
97.3    
97.5    
97.8    
98.1    
98.4    
98.6    
98.9    
99.2    
99.5    
99.7    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 8885, rend_intergenic: 6106  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14123, rend_intergenic: 11169  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23481, rend_intergenic: 21370  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40535, rend_intergenic: 25671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48103, rend_intergenic: 43820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66852, rend_intergenic: 61744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89013, rend_intergenic: 87743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98624, rend_intergenic: 93606  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103033, rend_intergenic: 99781  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107195, rend_intergenic: 103167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112298, rend_intergenic: 107214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126167, rend_intergenic: 112821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136879, rend_intergenic: 134685  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146164, rend_intergenic: 136896  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157367, rend_intergenic: 153777  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 160817 - 172198
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-found 1 predictions from path traversal

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