-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_10137298-10378920

-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: +)Couldn't classify 191967, 193067
Sorry, prediction pasa_asmbl_40268.p1 fails validation.
(CTT)	 AG	191967-193067	GG	CCG
Valid prediction for snap_scaffold_3-snap.2032-T1
Couldn't classify 164726, 164879
Sorry, prediction pasa_asmbl_40262.p1 fails validation.
(TTG)	 GT	164726-164879	GT	TGG
(GGG)	 AG	166850-166923	GT	AGG
(ATG)	 AG	167281-167465	GT	GCG
(GAT)	 AG	167595-167700	GT	AGG
(TTC)	 AG	168250-168366	GT	GCG
(TAA)	 AG	168798-168800	CA	AAC
-recovered pasa_asmbl_40262.p1, initial, 167281, 167465
-recovered pasa_asmbl_40262.p1, terminal, 168798, 168800
-recovered pasa_asmbl_40262.p1, internal, 166850, 166923
-recovered pasa_asmbl_40262.p1, internal, 167281, 167465
-recovered pasa_asmbl_40262.p1, internal, 167595, 167700
-recovered pasa_asmbl_40262.p1, internal, 168250, 168366
Valid prediction for Augustus_model.g4683.t1
Valid prediction for GlimmerHMM_glimmerT_7195-T1
Valid prediction for CodingQuarry_transcript_46244-T1
Valid prediction for GlimmerHMM_glimmerT_7213-T1
Valid prediction for GlimmerHMM_glimmerT_7211-T1
Valid prediction for snap_scaffold_3-snap.2022-T1
Valid prediction for GlimmerHMM_glimmerT_7176-T1
Valid prediction for GlimmerHMM_glimmerT_7186-T1
Valid prediction for HiQ_model.g4698.t1
Valid prediction for snap_scaffold_3-snap.2047-T1
Valid prediction for Augustus_model.g4676.t1
Valid prediction for HiQ_model.g4691.t1
Valid prediction for Augustus_model.g4686.t1
Valid prediction for CodingQuarry_transcript_46248-T1
Valid prediction for GlimmerHMM_glimmerT_7197-T1
Valid prediction for snap_scaffold_3-snap.2012-T1
Valid prediction for Augustus_model.g4680.t1
Valid prediction for HiQ_model.g4690.t1
Valid prediction for snap_scaffold_3-snap.2002-T1
Valid prediction for snap_scaffold_3-snap.2016-T1
Valid prediction for snap_scaffold_3-snap.2019-T1
Valid prediction for snap_scaffold_3-snap.2001-T1
Valid prediction for Augustus_model.g4693.t1
Valid prediction for GlimmerHMM_glimmerT_7183-T1
Valid prediction for Augustus_model.g4688.t1
Couldn't classify 105964, 106449
Sorry, prediction pasa_asmbl_40244.p1 fails validation.
(ACA)	 GG	105964-106449	CA	AGC
Valid prediction for snap_scaffold_3-snap.2037-T1
Valid prediction for snap_scaffold_3-snap.2004-T1
Valid prediction for snap_scaffold_3-snap.2007-T1
Valid prediction for GlimmerHMM_glimmerT_7189-T1
Valid prediction for snap_scaffold_3-snap.2014-T1
Valid prediction for GlimmerHMM_glimmerT_7180-T1
Valid prediction for Augustus_model.g4675.t1
Valid prediction for snap_scaffold_3-snap.2009-T1
Couldn't classify 104383, 105150
Sorry, prediction pasa_asmbl_40243.p1 fails validation.
(ATG)	 GA	104167-104256	GT	AGG
(GAT)	 AG	104383-105150	GA	TGG
-recovered pasa_asmbl_40243.p1, initial, 104167, 104256
Valid prediction for pasa_asmbl_40259.p1
Valid prediction for GlimmerHMM_glimmerT_7212-T1
Valid prediction for snap_scaffold_3-snap.2029-T1
Couldn't classify 142530, 142556
Couldn't classify 143823, 143975
Sorry, prediction pasa_asmbl_40821.p1 fails validation.
(CAA)	 TA	142530-142556	GT	AAG
(AGA)	 AG	143117-143184	GT	AGG
(ACA)	 AG	143555-143666	GC	AGG
(AGG)	 AG	143823-143975	GT	AGG
-recovered pasa_asmbl_40821.p1, internal, 143117, 143184
-recovered pasa_asmbl_40821.p1, internal, 143555, 143666
-recovered pasa_asmbl_40821.p1, internal, 143823, 143975
Valid prediction for GlimmerHMM_glimmerT_7200-T1
Valid prediction for GlimmerHMM_glimmerT_7179-T1
Valid prediction for Augustus_model.g4685.t1
Valid prediction for GlimmerHMM_glimmerT_7204-T1
Valid prediction for snap_scaffold_3-snap.2030-T1
Valid prediction for GlimmerHMM_glimmerT_7206-T1
Valid prediction for snap_scaffold_3-snap.2044-T1
Valid prediction for snap_scaffold_3-snap.2040-T1
Valid prediction for snap_scaffold_3-snap.2020-T1
Valid prediction for GlimmerHMM_glimmerT_7187-T1
Valid prediction for GlimmerHMM_glimmerT_7178-T1
Couldn't classify 111628, 111765
Sorry, prediction pasa_asmbl_40868.p1 fails validation.
(ATC)	 AG	111628-111765	GT	AGG
(GCC)	 AG	112494-112615	GT	CGG
(GGA)	 AG	112700-112876	GT	AGG
(ACT)	 AG	113051-113259	GT	CAG
(GTT)	 AG	114559-114777	GT	GGG
(AGC)	 AG	114912-115051	GT	CGG
(CTA)	 AG	115553-115754	GT	GGG
(GTG)	 AG	115973-116046	AC	GAA
-recovered pasa_asmbl_40868.p1, terminal, 115973, 116046
-recovered pasa_asmbl_40868.p1, internal, 111628, 111765
-recovered pasa_asmbl_40868.p1, internal, 112494, 112615
-recovered pasa_asmbl_40868.p1, internal, 112700, 112876
-recovered pasa_asmbl_40868.p1, internal, 113051, 113259
-recovered pasa_asmbl_40868.p1, internal, 114559, 114777
-recovered pasa_asmbl_40868.p1, internal, 114912, 115051
-recovered pasa_asmbl_40868.p1, internal, 115553, 115754
Valid prediction for GlimmerHMM_glimmerT_7188-T1
Valid prediction for GlimmerHMM_glimmerT_7192-T1
Valid prediction for snap_scaffold_3-snap.2026-T1
Valid prediction for snap_scaffold_3-snap.2043-T1
Valid prediction for Augustus_model.g4684.t1
Valid prediction for GlimmerHMM_glimmerT_7207-T1
Valid prediction for Augustus_model.g4679.t1
Valid prediction for snap_scaffold_3-snap.2021-T1
Valid prediction for GlimmerHMM_glimmerT_7182-T1
Valid prediction for snap_scaffold_3-snap.2028-T1
Valid prediction for GlimmerHMM_glimmerT_7194-T1
Valid prediction for GlimmerHMM_glimmerT_7175-T1
Valid prediction for Augustus_model.g4695.t1
Valid prediction for snap_scaffold_3-snap.2039-T1
Valid prediction for GlimmerHMM_glimmerT_7214-T1
Valid prediction for GlimmerHMM_glimmerT_7201-T1
Valid prediction for pasa_asmbl_40269.p1
Valid prediction for GlimmerHMM_glimmerT_7184-T1
Valid prediction for GlimmerHMM_glimmerT_7193-T1
Couldn't classify 136131, 136321
Sorry, prediction pasa_asmbl_40251.p1 fails validation.
(CCT)	 TC	136131-136321	GT	GGG
(TAA)	 AG	137273-137423	GT	AGG
(CAT)	 AG	138294-138386	GT	AGG
(CTA)	 AG	138671-138719	GT	TGG
(TGG)	 AG	138809-138884	GT	AAG
(GAA)	 AG	140388-140502	AC	AAA
-recovered pasa_asmbl_40251.p1, terminal, 140388, 140502
-recovered pasa_asmbl_40251.p1, internal, 137273, 137423
-recovered pasa_asmbl_40251.p1, internal, 138294, 138386
-recovered pasa_asmbl_40251.p1, internal, 138671, 138719
-recovered pasa_asmbl_40251.p1, internal, 138809, 138884
Valid prediction for snap_scaffold_3-snap.2033-T1
Valid prediction for CodingQuarry_transcript_46245-T1
Couldn't classify 156269, 157684
Sorry, prediction pasa_asmbl_40258.p1 fails validation.
(ATT)	 GC	156269-157684	CC	GCC
Couldn't classify 110753, 110915
Couldn't classify 111345, 111422
Sorry, prediction pasa_asmbl_40892.p1 fails validation.
(GAG)	 AG	110753-110915	GT	CGG
(AGT)	 AG	111119-111219	GT	AGG
(GAG)	 AG	111345-111422	GT	AGG
-recovered pasa_asmbl_40892.p1, internal, 110753, 110915
-recovered pasa_asmbl_40892.p1, internal, 111119, 111219
-recovered pasa_asmbl_40892.p1, internal, 111345, 111422
Valid prediction for snap_scaffold_3-snap.2036-T1
Couldn't classify 106645, 106776
Couldn't classify 108193, 108249
Sorry, prediction pasa_asmbl_40245.p1 fails validation.
(AGG)	 AT	106645-106776	GT	AGG
(TCT)	 AG	106964-107024	GT	CGG
(CCC)	 AG	107381-107481	GT	AGG
(GCT)	 AG	107648-107746	GT	AGG
(AAC)	 AG	108193-108249	GG	GGG
-recovered pasa_asmbl_40245.p1, internal, 106964, 107024
-recovered pasa_asmbl_40245.p1, internal, 107381, 107481
-recovered pasa_asmbl_40245.p1, internal, 107648, 107746

-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.g4682.t1
Valid prediction for GlimmerHMM_glimmerT_7202-T1
Valid prediction for snap_scaffold_3-snap.2015-T1
Valid prediction for snap_scaffold_3-snap.2008-T1
Valid prediction for snap_scaffold_3-snap.2027-T1
Valid prediction for GlimmerHMM_glimmerT_7191-T1
Valid prediction for GlimmerHMM_glimmerT_7190-T1
Valid prediction for Augustus_model.g4678.t1
Valid prediction for snap_scaffold_3-snap.2005-T1
Valid prediction for Augustus_model.g4697.t1
Valid prediction for snap_scaffold_3-snap.2048-T1
Valid prediction for GlimmerHMM_glimmerT_7196-T1
Valid prediction for snap_scaffold_3-snap.2023-T1
Valid prediction for GlimmerHMM_glimmerT_7177-T1
Valid prediction for GlimmerHMM_glimmerT_7198-T1
Valid prediction for snap_scaffold_3-snap.2041-T1
Valid prediction for Augustus_model.g4694.t1
Valid prediction for snap_scaffold_3-snap.2038-T1
Valid prediction for snap_scaffold_3-snap.2011-T1
Valid prediction for snap_scaffold_3-snap.2045-T1
Valid prediction for GlimmerHMM_glimmerT_7205-T1
Valid prediction for Augustus_model.g4689.t1
Valid prediction for snap_scaffold_3-snap.2025-T1
Valid prediction for snap_scaffold_3-snap.2035-T1
Valid prediction for snap_scaffold_3-snap.2042-T1
Valid prediction for GlimmerHMM_glimmerT_7210-T1
Valid prediction for GlimmerHMM_glimmerT_7203-T1
Valid prediction for snap_scaffold_3-snap.2018-T1
Valid prediction for snap_scaffold_3-snap.2017-T1
Valid prediction for Augustus_model.g4677.t1
Valid prediction for snap_scaffold_3-snap.2010-T1
Valid prediction for GlimmerHMM_glimmerT_7209-T1
Valid prediction for GlimmerHMM_glimmerT_7199-T1
Valid prediction for Augustus_model.g4681.t1
Valid prediction for GlimmerHMM_glimmerT_7181-T1
Valid prediction for snap_scaffold_3-snap.2046-T1
Valid prediction for snap_scaffold_3-snap.2013-T1
Valid prediction for Augustus_model.g4687.t1
Valid prediction for GlimmerHMM_glimmerT_7208-T1
Valid prediction for snap_scaffold_3-snap.2024-T1
Valid prediction for snap_scaffold_3-snap.2034-T1
Valid prediction for GlimmerHMM_glimmerT_7185-T1
Valid prediction for snap_scaffold_3-snap.2031-T1
Valid prediction for Augustus_model.g4692.t1
Valid prediction for Augustus_model.g4674.t1
Valid prediction for Augustus_model.g4696.t1
Valid prediction for snap_scaffold_3-snap.2006-T1
Valid prediction for snap_scaffold_3-snap.2003-T1
Valid prediction for snap_scaffold_3-snap.2000-T1
Valid prediction for CodingQuarry_transcript_46246-T1
Couldn't classify 70026, 70084
Sorry, prediction pasa_asmbl_39075.p1 fails validation.
(GTG)	 TG	70026-70084	GT	AAG
(GCT)	 AG	70598-70697	GT	ATG
(TTG)	 AG	70900-71043	GT	TGG
(ACG)	 AG	71439-71573	CA	AGC
-recovered pasa_asmbl_39075.p1, terminal, 71439, 71573
-recovered pasa_asmbl_39075.p1, internal, 70598, 70697
-recovered pasa_asmbl_39075.p1, internal, 70900, 71043

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12144, rend_intergenic: 3086  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12704, rend_intergenic: 12620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17366, rend_intergenic: 13064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28577, rend_intergenic: 24143  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38103, rend_intergenic: 30341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43422, rend_intergenic: 38675  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46100, rend_intergenic: 45472  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48540, rend_intergenic: 46235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64119, rend_intergenic: 56734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116046, rend_intergenic: 104773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126269, rend_intergenic: 121890  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130899, rend_intergenic: 126419  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134668, rend_intergenic: 132440  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180701, rend_intergenic: 174676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193106, rend_intergenic: 191154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196965, rend_intergenic: 194263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202195, rend_intergenic: 199316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209958, rend_intergenic: 208021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 240707, rend_intergenic: 233750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 241623
-exon list size: 477


building trellis

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94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 43 predictions from path traversal
Error with prediction: snap lend_intergenic: 12144, rend_intergenic: 3086  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12704, rend_intergenic: 12620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17366, rend_intergenic: 13064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28577, rend_intergenic: 24143  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38103, rend_intergenic: 30341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43422, rend_intergenic: 38675  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46100, rend_intergenic: 45472  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48540, rend_intergenic: 46235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64119, rend_intergenic: 56734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116046, rend_intergenic: 104773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126269, rend_intergenic: 121890  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130899, rend_intergenic: 126419  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134668, rend_intergenic: 132440  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180701, rend_intergenic: 174676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193106, rend_intergenic: 191154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196965, rend_intergenic: 194263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202195, rend_intergenic: 199316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209958, rend_intergenic: 208021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 240707, rend_intergenic: 233750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 16011
-exon list size: 20


building trellis

4.5    
9.1    
13.6    
18.2    
22.7    
27.3    
31.8    
36.4    
40.9    
45.5    
50.0    
54.5    
59.1    
63.6    
68.2    
72.7    
77.3    
81.8    
86.4    
90.9    
95.5    
-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 1 - 14342
-exon list size: 17


building trellis

5.3    
10.5    
15.8    
21.1    
26.3    
31.6    
36.8    
42.1    
47.4    
52.6    
57.9    
63.2    
68.4    
73.7    
78.9    
84.2    
89.5    
94.7    
-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

-building DP trellis

-building trellis in range 1 - 12689
-exon list size: 13


building trellis

6.7    
13.3    
20.0    
26.7    
33.3    
40.0    
46.7    
53.3    
60.0    
66.7    
73.3    
80.0    
86.7    
93.3    
-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