-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_8/scaffold_8_9956514-10205358

-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 GeneMark_model.35596_t
Valid prediction for GeneMark_model.35589_t
Valid prediction for GlimmerHMM_glimmerT_20842-T1
Valid prediction for Augustus_model.g13955.t1
Valid prediction for GlimmerHMM_glimmerT_20826-T1
Valid prediction for GeneMark_model.35601_t
Valid prediction for snap_scaffold_8-snap.2004-T1
Valid prediction for GeneMark_model.35594_t
Valid prediction for Augustus_model.g13939.t1
Valid prediction for Augustus_model.g13937.t1
Valid prediction for Augustus_model.g13940.t1
Couldn't classify 188353, 188391
Couldn't classify 194531, 194560
Sorry, prediction pasa_asmbl_52138.p1 fails validation.
(GCC)	 GA	188353-188391	GT	AGG
(GTC)	 AG	189223-189291	GT	AGG
(TGT)	 AG	189556-189637	GT	TGG
(GTG)	 AG	190407-190468	GT	CGG
(GTT)	 AG	191485-191533	GT	AGG
(ATG)	 AG	191666-191739	GT	AGG
(TTG)	 AG	192947-192997	GT	CAG
(CCT)	 AG	193184-193255	GT	AGG
(CTG)	 AG	194531-194560	GC	AGG
add_exon() Sorry, pasa_asmbl_52138.p1 191666-191739-initial-1 is invalid.
-recovered pasa_asmbl_52138.p1, initial, 191666, 191739
-recovered pasa_asmbl_52138.p1, internal, 189223, 189291
-recovered pasa_asmbl_52138.p1, internal, 189556, 189637
-recovered pasa_asmbl_52138.p1, internal, 190407, 190468
-recovered pasa_asmbl_52138.p1, internal, 191485, 191533
-recovered pasa_asmbl_52138.p1, internal, 191666, 191739
-recovered pasa_asmbl_52138.p1, internal, 192947, 192997
-recovered pasa_asmbl_52138.p1, internal, 193184, 193255
-recovered pasa_asmbl_52138.p1, internal, 194531, 194560
Valid prediction for snap_scaffold_8-snap.2003-T1
Valid prediction for GeneMark_model.35583_t
Valid prediction for snap_scaffold_8-snap.1970-T1
Valid prediction for GlimmerHMM_glimmerT_20845-T1
Valid prediction for snap_scaffold_8-snap.1966-T1
Couldn't classify 139855, 140442
Sorry, prediction pasa_asmbl_52131.p1 fails validation.
(TCA)	 CT	139855-140442	CG	AGC
Valid prediction for snap_scaffold_8-snap.1981-T1
Valid prediction for snap_scaffold_8-snap.1985-T1
Valid prediction for Augustus_model.g13954.t1
Valid prediction for GeneMark_model.35582_t
Valid prediction for Augustus_model.g13936.t1
Valid prediction for GeneMark_model.35581_t
Valid prediction for snap_scaffold_8-snap.2005-T1
Valid prediction for snap_scaffold_8-snap.1975-T1
Valid prediction for GeneMark_model.35597_t
Valid prediction for GeneMark_model.35604_t
Valid prediction for GlimmerHMM_glimmerT_20824-T1
Valid prediction for Augustus_model.g13956.t1
Valid prediction for GlimmerHMM_glimmerT_20828-T1
Valid prediction for snap_scaffold_8-snap.1964-T1
Valid prediction for Augustus_model.g13957.t1
Valid prediction for GeneMark_model.35599_t
Valid prediction for Augustus_model.g13958.t1
Couldn't classify 2683, 3174
Sorry, prediction pasa_asmbl_52122.p1 fails validation.
(AGT)	 CA	2683-3174	TG	AGT
Valid prediction for snap_scaffold_8-snap.1990-T1
Valid prediction for snap_scaffold_8-snap.2000-T1
Valid prediction for snap_scaffold_8-snap.2002-T1
Valid prediction for GlimmerHMM_glimmerT_20843-T1
Valid prediction for snap_scaffold_8-snap.1976-T1
Valid prediction for GlimmerHMM_glimmerT_20832-T1
Valid prediction for GeneMark_model.35609_t
Valid prediction for GeneMark_model.35600_t
Valid prediction for GeneMark_model.35574_t
Couldn't classify 56961, 56988
Sorry, prediction pasa_asmbl_52128.p1 fails validation.
(GAA)	 TG	56961-56988	GT	AGG
(AGC)	 AG	58456-58602	GT	ACG
(AGC)	 AG	59553-59690	GT	AGG
(GCC)	 AG	61218-61372	GG	GAG
-recovered pasa_asmbl_52128.p1, terminal, 61218, 61372
-recovered pasa_asmbl_52128.p1, internal, 58456, 58602
-recovered pasa_asmbl_52128.p1, internal, 59553, 59690
Valid prediction for snap_scaffold_8-snap.2001-T1
Valid prediction for GlimmerHMM_glimmerT_20827-T1
Valid prediction for Augustus_model.g13943.t1
Valid prediction for snap_scaffold_8-snap.1999-T1
Valid prediction for Augustus_model.g13953.t1
Valid prediction for snap_scaffold_8-snap.1973-T1
Valid prediction for GlimmerHMM_glimmerT_20831-T1
Valid prediction for GeneMark_model.35578_t
Valid prediction for snap_scaffold_8-snap.1978-T1
Valid prediction for GlimmerHMM_glimmerT_20844-T1
Valid prediction for GeneMark_model.35577_t
Couldn't classify 27104, 27709
Sorry, prediction pasa_asmbl_52123.p1 fails validation.
(ACC)	 AG	27104-27709	GA	CGG
Valid prediction for GeneMark_model.35585_t
Valid prediction for snap_scaffold_8-snap.1996-T1
Valid prediction for HiQ_model.g13942.t1
Valid prediction for GlimmerHMM_glimmerT_20829-T1
Valid prediction for GlimmerHMM_glimmerT_20830-T1
Valid prediction for CodingQuarry_transcript_59643-T1
Valid prediction for snap_scaffold_8-snap.1994-T1
Couldn't classify 49854, 50005
Sorry, prediction pasa_asmbl_52125.p1 fails validation.
(TTG)	 CC	49854-50005	GT	AGG
(CTC)	 AG	52628-52784	GT	AGG
(GCG)	 AG	53154-53282	GT	GGG
(AAC)	 AG	53388-53447	GT	TGG
(TCC)	 AG	53537-53698	GT	CTG
(AAA)	 AG	53806-53910	GT	AGG
(AAA)	 AG	54084-54234	GT	TGG
(GTG)	 AG	54323-54488	GT	TGG
(GTT)	 AG	54570-54720	GT	AGG
(GTG)	 AG	54821-54943	AG	AGA
-recovered pasa_asmbl_52125.p1, terminal, 54821, 54943
-recovered pasa_asmbl_52125.p1, internal, 52628, 52784
-recovered pasa_asmbl_52125.p1, internal, 53154, 53282
-recovered pasa_asmbl_52125.p1, internal, 53388, 53447
-recovered pasa_asmbl_52125.p1, internal, 53537, 53698
-recovered pasa_asmbl_52125.p1, internal, 53806, 53910
-recovered pasa_asmbl_52125.p1, internal, 54084, 54234
-recovered pasa_asmbl_52125.p1, internal, 54323, 54488
-recovered pasa_asmbl_52125.p1, internal, 54570, 54720
Valid prediction for snap_scaffold_8-snap.1967-T1
Valid prediction for Augustus_model.g13959.t1
Valid prediction for snap_scaffold_8-snap.1968-T1
Valid prediction for Augustus_model.g13941.t1
Couldn't classify 28004, 28237
Couldn't classify 28490, 28606
Sorry, prediction pasa_asmbl_52562.p1 fails validation.
(TTG)	 AG	28004-28237	GT	AGG
(GTG)	 AG	28490-28606	CG	AGC
-recovered pasa_asmbl_52562.p1, internal, 28004, 28237
Valid prediction for GlimmerHMM_glimmerT_20840-T1
Valid prediction for GeneMark_model.35587_t
Valid prediction for snap_scaffold_8-snap.1963-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_8-snap.1984-T1
Valid prediction for CodingQuarry_transcript_59635-T1
Couldn't classify 184299, 184460
Sorry, prediction pasa_asmbl_53085.p1 fails validation.
(ATG)	 GG	179901-180011	GT	GGG
(AAC)	 AG	180532-180616	GT	AGG
(GTT)	 AG	180731-180799	GT	AGG
(ATG)	 AG	180969-181087	GT	AGG
(GCC)	 AG	181494-181643	GT	TGG
(GTG)	 AG	181826-181900	GT	TGG
(AGC)	 AG	182000-182124	GT	GGG
(AAC)	 AG	182210-182483	GT	AGG
(GGG)	 AG	182583-182720	GT	GGG
(GTT)	 AG	182925-183078	GT	TGG
(GAT)	 AG	183179-183286	GT	AGG
(GTC)	 AG	183611-183736	GT	AGG
(GGG)	 AG	183840-183950	GT	AGG
(GCC)	 AG	184069-184184	GT	AGG
(GTG)	 AG	184299-184460	GA	AGG
-recovered pasa_asmbl_53085.p1, initial, 179901, 180011
-recovered pasa_asmbl_53085.p1, initial, 180969, 181087
add_exon() Sorry, pasa_asmbl_53085.p1 183179-183286-terminal-1 is invalid.
-recovered pasa_asmbl_53085.p1, terminal, 183179, 183286
-recovered pasa_asmbl_53085.p1, internal, 180532, 180616
-recovered pasa_asmbl_53085.p1, internal, 180731, 180799
-recovered pasa_asmbl_53085.p1, internal, 180969, 181087
-recovered pasa_asmbl_53085.p1, internal, 181494, 181643
-recovered pasa_asmbl_53085.p1, internal, 181826, 181900
-recovered pasa_asmbl_53085.p1, internal, 182000, 182124
-recovered pasa_asmbl_53085.p1, internal, 182210, 182483
-recovered pasa_asmbl_53085.p1, internal, 182583, 182720
-recovered pasa_asmbl_53085.p1, internal, 182925, 183078
-recovered pasa_asmbl_53085.p1, internal, 183179, 183286
-recovered pasa_asmbl_53085.p1, internal, 183611, 183736
-recovered pasa_asmbl_53085.p1, internal, 183840, 183950
-recovered pasa_asmbl_53085.p1, internal, 184069, 184184
Valid prediction for GeneMark_model.35608_t
Valid prediction for GlimmerHMM_glimmerT_20837-T1
Valid prediction for GlimmerHMM_glimmerT_20835-T1
Valid prediction for HiQ_model.g13945.t1
Valid prediction for snap_scaffold_8-snap.1986-T1
Valid prediction for snap_scaffold_8-snap.1971-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.35603_t
Valid prediction for GeneMark_model.35598_t
Valid prediction for HiQ_model.g13950.t1
Valid prediction for snap_scaffold_8-snap.1997-T1
Valid prediction for CodingQuarry_transcript_59639-T1
Valid prediction for HiQ_model.g13947.t1
Valid prediction for Augustus_model.g13938.t1
Valid prediction for GlimmerHMM_glimmerT_20833-T1
Valid prediction for snap_scaffold_8-snap.1989-T1
Valid prediction for GeneMark_model.35588_t
Valid prediction for CodingQuarry_transcript_59640-T1
Valid prediction for Augustus_model.g13946.t1
Valid prediction for HiQ_model.g13944.t1
Valid prediction for GeneMark_model.35595_t
Valid prediction for GeneMark_model.35575_t
Valid prediction for GeneMark_model.35605_t
Valid prediction for CodingQuarry_transcript_59634-T1
Valid prediction for snap_scaffold_8-snap.1977-T1
Valid prediction for snap_scaffold_8-snap.1969-T1
Valid prediction for snap_scaffold_8-snap.1972-T1
Couldn't classify 177903, 177904
Sorry, prediction CodingQuarry_transcript_59636-T1 fails validation.
(ATG)	 AG	174328-174433	GT	TGG
(AAC)	 AG	175162-175256	GT	TGG
(GAC)	 AG	175429-175578	GT	AGG
(GAC)	 AG	175938-176079	GT	AGG
(GCT)	 AG	176253-176417	GT	GAG
(GGG)	 AG	176608-176735	GT	AGG
(GTG)	 AG	176857-176970	GT	GGG
(AAG)	 AG	177147-177227	GT	AGG
(CTG)	 AG	177629-177764	GT	CTG
(AGG)	 AG	177903-177904	GT	AGG
-recovered CodingQuarry_transcript_59636-T1, initial, 174328, 174433
add_exon() Sorry, CodingQuarry_transcript_59636-T1 176253-176417-terminal-1 is invalid.
-recovered CodingQuarry_transcript_59636-T1, terminal, 176253, 176417
-recovered CodingQuarry_transcript_59636-T1, internal, 174328, 174433
-recovered CodingQuarry_transcript_59636-T1, internal, 175162, 175256
-recovered CodingQuarry_transcript_59636-T1, internal, 175429, 175578
-recovered CodingQuarry_transcript_59636-T1, internal, 175938, 176079
-recovered CodingQuarry_transcript_59636-T1, internal, 176253, 176417
-recovered CodingQuarry_transcript_59636-T1, internal, 176608, 176735
-recovered CodingQuarry_transcript_59636-T1, internal, 176857, 176970
-recovered CodingQuarry_transcript_59636-T1, internal, 177147, 177227
-recovered CodingQuarry_transcript_59636-T1, internal, 177629, 177764
-recovered CodingQuarry_transcript_59636-T1, internal, 177903, 177904
Valid prediction for GlimmerHMM_glimmerT_20834-T1
Valid prediction for Augustus_model.g13952.t1
Valid prediction for pasa_asmbl_53092.p1
Valid prediction for snap_scaffold_8-snap.1993-T1
Valid prediction for snap_scaffold_8-snap.1983-T1
Couldn't classify 184700, 184792
Sorry, prediction pasa_asmbl_53084.p1 fails validation.
(CAG)	 CA	184700-184792	GT	AGG
(GTG)	 AG	184885-185109	AC	AGA
-recovered pasa_asmbl_53084.p1, terminal, 184885, 185109
Valid prediction for GeneMark_model.35590_t
Valid prediction for GlimmerHMM_glimmerT_20841-T1
Valid prediction for snap_scaffold_8-snap.1982-T1
Valid prediction for pasa_asmbl_53093.p1
Valid prediction for GlimmerHMM_glimmerT_20825-T1
Valid prediction for snap_scaffold_8-snap.1992-T1
Valid prediction for GeneMark_model.35584_t
Valid prediction for snap_scaffold_8-snap.1980-T1
Valid prediction for Augustus_model.g13949.t1
Valid prediction for GeneMark_model.35593_t
Valid prediction for snap_scaffold_8-snap.1974-T1
Valid prediction for CodingQuarry_transcript_59638-T1
Valid prediction for GeneMark_model.35586_t
Valid prediction for GeneMark_model.35592_t
Valid prediction for snap_scaffold_8-snap.1979-T1
Valid prediction for pasa_asmbl_53086.p1
Valid prediction for GlimmerHMM_glimmerT_20836-T1
Valid prediction for snap_scaffold_8-snap.1998-T1
Valid prediction for snap_scaffold_8-snap.1965-T1
Valid prediction for snap_scaffold_8-snap.1991-T1
Valid prediction for GeneMark_model.35606_t
Valid prediction for GeneMark_model.35602_t
Valid prediction for CodingQuarry_transcript_59641-T1
Valid prediction for snap_scaffold_8-snap.1987-T1
Valid prediction for CodingQuarry_transcript_59637-T1
Valid prediction for GeneMark_model.35580_t
Valid prediction for Augustus_model.g13951.t1
Valid prediction for GeneMark_model.35579_t
Valid prediction for GlimmerHMM_glimmerT_20838-T1
Valid prediction for snap_scaffold_8-snap.1995-T1
Valid prediction for snap_scaffold_8-snap.1988-T1
Valid prediction for GeneMark_model.35576_t
Valid prediction for HiQ_model.g13948.t1
Valid prediction for GlimmerHMM_glimmerT_20839-T1
Valid prediction for pasa_asmbl_53091.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 23279, rend_intergenic: 22666  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29548, rend_intergenic: 28469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37842, rend_intergenic: 33753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45913, rend_intergenic: 41564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58640, rend_intergenic: 54529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74518, rend_intergenic: 70569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93049, rend_intergenic: 87366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118708, rend_intergenic: 106439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157751, rend_intergenic: 150625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 248845
-exon list size: 572


building trellis

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67.4    
67.6    
67.8    
67.9    
68.1    
68.3    
68.5    
68.6    
68.8    
69.0    
69.2    
69.3    
69.5    
69.7    
69.9    
70.0    
70.2    
70.4    
70.6    
70.7    
70.9    
71.1    
71.3    
71.4    
71.6    
71.8    
72.0    
72.1    
72.3    
72.5    
72.6    
72.8    
73.0    
73.2    
73.3    
73.5    
73.7    
73.9    
74.0    
74.2    
74.4    
74.6    
74.7    
74.9    
75.1    
75.3    
75.4    
75.6    
75.8    
76.0    
76.1    
76.3    
76.5    
76.7    
76.8    
77.0    
77.2    
77.4    
77.5    
77.7    
77.9    
78.0    
78.2    
78.4    
78.6    
78.7    
78.9    
79.1    
79.3    
79.4    
79.6    
79.8    
80.0    
80.1    
80.3    
80.5    
80.7    
80.8    
81.0    
81.2    
81.4    
81.5    
81.7    
81.9    
82.1    
82.2    
82.4    
82.6    
82.8    
82.9    
83.1    
83.3    
83.4    
83.6    
83.8    
84.0    
84.1    
84.3    
84.5    
84.7    
84.8    
85.0    
85.2    
85.4    
85.5    
85.7    
85.9    
86.1    
86.2    
86.4    
86.6    
86.8    
86.9    
87.1    
87.3    
87.5    
87.6    
87.8    
88.0    
88.2    
88.3    
88.5    
88.7    
88.9    
89.0    
89.2    
89.4    
89.5    
89.7    
89.9    
90.1    
90.2    
90.4    
90.6    
90.8    
90.9    
91.1    
91.3    
91.5    
91.6    
91.8    
92.0    
92.2    
92.3    
92.5    
92.7    
92.9    
93.0    
93.2    
93.4    
93.6    
93.7    
93.9    
94.1    
94.3    
94.4    
94.6    
94.8    
94.9    
95.1    
95.3    
95.5    
95.6    
95.8    
96.0    
96.2    
96.3    
96.5    
96.7    
96.9    
97.0    
97.2    
97.4    
97.6    
97.7    
97.9    
98.1    
98.3    
98.4    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 23279, rend_intergenic: 22666  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29548, rend_intergenic: 28469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37842, rend_intergenic: 33753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45913, rend_intergenic: 41564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58640, rend_intergenic: 54529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74518, rend_intergenic: 70569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93049, rend_intergenic: 87366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118708, rend_intergenic: 106439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157751, rend_intergenic: 150625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support