-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_7/scaffold_7_10167345-10432456

-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_18420-T1
Couldn't classify 157334, 157831
Sorry, prediction pasa_asmbl_50995.p1 fails validation.
(TAT)	 TC	157334-157831	TT	AGT
Valid prediction for Augustus_model.g12409.t1
Valid prediction for GlimmerHMM_glimmerT_18409-T1
Valid prediction for Augustus_model.g12420.t1
Couldn't classify 237124, 237229
Sorry, prediction pasa_asmbl_50999.p1 fails validation.
(TTT)	 GG	237124-237229	GT	AGG
(TCC)	 AG	239906-239989	GT	AGG
(AGG)	 AG	241690-241807	GT	AGG
(GTA)	 AG	241963-242294	GT	TGG
(GCT)	 AG	242397-242446	GT	TGG
(GGA)	 AG	242572-242691	GT	ATG
(GTG)	 AG	242809-244758	GA	AGG
-recovered pasa_asmbl_50999.p1, terminal, 242809, 244758
-recovered pasa_asmbl_50999.p1, internal, 239906, 239989
-recovered pasa_asmbl_50999.p1, internal, 241690, 241807
-recovered pasa_asmbl_50999.p1, internal, 241963, 242294
-recovered pasa_asmbl_50999.p1, internal, 242397, 242446
-recovered pasa_asmbl_50999.p1, internal, 242572, 242691
Valid prediction for snap_scaffold_7-snap.1982-T1
Valid prediction for GeneMark_model.30879_t
Valid prediction for snap_scaffold_7-snap.2005-T1
Valid prediction for GeneMark_model.30850_t
Valid prediction for GlimmerHMM_glimmerT_18396-T1
Valid prediction for snap_scaffold_7-snap.1997-T1
Valid prediction for GeneMark_model.30885_t
Valid prediction for snap_scaffold_7-snap.1989-T1
Valid prediction for GeneMark_model.30862_t
Valid prediction for Augustus_model.g12417.t1
Valid prediction for GlimmerHMM_glimmerT_18411-T1
Valid prediction for snap_scaffold_7-snap.1970-T1
Valid prediction for Augustus_model.g12421.t1
Valid prediction for snap_scaffold_7-snap.1968-T1
Couldn't classify 148644, 148700
Sorry, prediction pasa_asmbl_50993.p2 fails validation.
(GCT)	 AA	148644-148700	GT	TGG
(ATG)	 AG	148823-148841	GT	AGG
(ATG)	 AG	149260-149534	AA	GAA
-recovered pasa_asmbl_50993.p2, initial, 148823, 148841
-recovered pasa_asmbl_50993.p2, terminal, 149260, 149534
-recovered pasa_asmbl_50993.p2, internal, 148823, 148841
Valid prediction for snap_scaffold_7-snap.1992-T1
Valid prediction for GeneMark_model.30847_t
Valid prediction for GlimmerHMM_glimmerT_18413-T1
Valid prediction for HiQ_model.g12406.t1
Valid prediction for GlimmerHMM_glimmerT_18407-T1
Valid prediction for GlimmerHMM_glimmerT_18398-T1
Valid prediction for Augustus_model.g12414.t1
Valid prediction for GeneMark_model.30863_t
Valid prediction for GlimmerHMM_glimmerT_18408-T1
Valid prediction for GeneMark_model.30871_t
Valid prediction for GlimmerHMM_glimmerT_18421-T1
Valid prediction for GlimmerHMM_glimmerT_18415-T1
Valid prediction for Augustus_model.g12407.t1
Valid prediction for snap_scaffold_7-snap.1986-T1
Couldn't classify 148152, 148209
Sorry, prediction pasa_asmbl_50992.p1 fails validation.
(ATG)	 CA	146891-146929	GT	TGG
(TGT)	 AG	147360-147498	GT	TGG
(GTC)	 AG	147670-147804	GT	AGG
(CTA)	 AG	147932-148049	GT	ACG
(GTG)	 AG	148152-148209	GA	ATG
-recovered pasa_asmbl_50992.p1, initial, 146891, 146929
-recovered pasa_asmbl_50992.p1, internal, 147360, 147498
-recovered pasa_asmbl_50992.p1, internal, 147670, 147804
-recovered pasa_asmbl_50992.p1, internal, 147932, 148049
Valid prediction for GeneMark_model.30857_t
Valid prediction for GeneMark_model.30856_t
Valid prediction for snap_scaffold_7-snap.1999-T1
Couldn't classify 187411, 187546
Couldn't classify 188270, 188331
Sorry, prediction pasa_asmbl_50996.p1 fails validation.
(AGT)	 TC	187411-187546	GT	CAG
(GTG)	 AG	187688-187888	GT	GAG
(ACC)	 AG	188012-188176	GT	AAG
(CGC)	 AG	188270-188331	GG	AAG
-recovered pasa_asmbl_50996.p1, internal, 187688, 187888
-recovered pasa_asmbl_50996.p1, internal, 188012, 188176
Valid prediction for snap_scaffold_7-snap.1988-T1
Valid prediction for snap_scaffold_7-snap.1985-T1
Valid prediction for GeneMark_model.30872_t
Valid prediction for GeneMark_model.30881_t
Valid prediction for snap_scaffold_7-snap.1976-T1
Valid prediction for snap_scaffold_7-snap.1994-T1
Valid prediction for Augustus_model.g12408.t1
Valid prediction for GlimmerHMM_glimmerT_18397-T1
Valid prediction for GeneMark_model.30864_t
Valid prediction for snap_scaffold_7-snap.1995-T1
Valid prediction for pasa_asmbl_50994.p1
Valid prediction for GeneMark_model.30854_t
Valid prediction for HiQ_model.g12410.t1
Valid prediction for GeneMark_model.30861_t
Valid prediction for GeneMark_model.30869_t
Valid prediction for snap_scaffold_7-snap.1987-T1
Valid prediction for pasa_asmbl_50985.p1
Valid prediction for snap_scaffold_7-snap.1984-T1
Valid prediction for snap_scaffold_7-snap.2004-T1
Valid prediction for GeneMark_model.30873_t
Valid prediction for GlimmerHMM_glimmerT_18406-T1
Valid prediction for CodingQuarry_transcript_57461-T1
Valid prediction for GlimmerHMM_glimmerT_18416-T1
Valid prediction for snap_scaffold_7-snap.1971-T1
Valid prediction for GeneMark_model.30875_t
Valid prediction for snap_scaffold_7-snap.2002-T1
Valid prediction for Augustus_model.g12412.t1
Valid prediction for GlimmerHMM_glimmerT_18401-T1
Couldn't classify 131077, 131159
Sorry, prediction pasa_asmbl_50990.p1 fails validation.
(ATC)	 AT	131077-131159	GT	CGG
(GTT)	 AG	131345-131389	GT	CTG
(CTG)	 AG	131484-131527	GT	AGG
(TTG)	 AG	131753-131991	GT	AGG
(GGA)	 AG	132162-132303	GT	CAG
(ACC)	 AG	134348-134514	GT	AGG
(GAC)	 AG	134791-135054	GT	AGG
(GTG)	 AG	135208-135393	AA	GAA
-recovered pasa_asmbl_50990.p1, terminal, 135208, 135393
-recovered pasa_asmbl_50990.p1, internal, 131345, 131389
-recovered pasa_asmbl_50990.p1, internal, 131484, 131527
-recovered pasa_asmbl_50990.p1, internal, 131753, 131991
-recovered pasa_asmbl_50990.p1, internal, 132162, 132303
-recovered pasa_asmbl_50990.p1, internal, 134348, 134514
-recovered pasa_asmbl_50990.p1, internal, 134791, 135054
Valid prediction for snap_scaffold_7-snap.1990-T1
Valid prediction for Augustus_model.g12415.t1
Valid prediction for GeneMark_model.30883_t
Valid prediction for snap_scaffold_7-snap.1980-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 GeneMark_model.30874_t
Couldn't classify 68189, 68368
Sorry, prediction pasa_asmbl_49934.p1 fails validation.
(ATG)	 GC	66002-67186	GT	AGG
(GAC)	 AG	67380-67510	GT	AGG
(GCG)	 AG	67860-67983	GT	CAG
(GGG)	 AG	68189-68368	GT	AGG
-recovered pasa_asmbl_49934.p1, initial, 66002, 67186
-recovered pasa_asmbl_49934.p1, internal, 67380, 67510
-recovered pasa_asmbl_49934.p1, internal, 67860, 67983
-recovered pasa_asmbl_49934.p1, internal, 68189, 68368
Valid prediction for GlimmerHMM_glimmerT_18402-T1
Valid prediction for GlimmerHMM_glimmerT_18395-T1
Valid prediction for Augustus_model.g12399.t1
Valid prediction for GeneMark_model.30853_t
Valid prediction for GlimmerHMM_glimmerT_18403-T1
Valid prediction for CodingQuarry_transcript_57462-T1
Valid prediction for snap_scaffold_7-snap.2007-T1
Valid prediction for Augustus_model.g12419.t1
Valid prediction for snap_scaffold_7-snap.1998-T1
Valid prediction for Augustus_model.g12401.t1
Valid prediction for snap_scaffold_7-snap.1967-T1
Valid prediction for GeneMark_model.30878_t
Valid prediction for GeneMark_model.30848_t
Valid prediction for HiQ_model.g12416.t1
Valid prediction for CodingQuarry_transcript_57465-T1
Valid prediction for snap_scaffold_7-snap.1993-T1
Valid prediction for GeneMark_model.30858_t
Valid prediction for CodingQuarry_transcript_57464-T1
Valid prediction for snap_scaffold_7-snap.2006-T1
Valid prediction for GlimmerHMM_glimmerT_18418-T1
Valid prediction for Augustus_model.g12403.t1
Valid prediction for snap_scaffold_7-snap.2001-T1
Valid prediction for GlimmerHMM_glimmerT_18400-T1
Valid prediction for GeneMark_model.30846_t
Valid prediction for GlimmerHMM_glimmerT_18422-T1
Valid prediction for GeneMark_model.30851_t
Valid prediction for GlimmerHMM_glimmerT_18419-T1
Valid prediction for snap_scaffold_7-snap.1974-T1
Valid prediction for CodingQuarry_transcript_57460-T1
Valid prediction for Augustus_model.g12418.t1
Valid prediction for Augustus_model.g12411.t1
Valid prediction for snap_scaffold_7-snap.1996-T1
Valid prediction for GlimmerHMM_glimmerT_18410-T1
Valid prediction for CodingQuarry_transcript_57463-T1
Valid prediction for GeneMark_model.30882_t
Couldn't classify 72133, 72262
Sorry, prediction pasa_asmbl_49933.p1 fails validation.
(GAG)	 AG	72133-72262	GT	AGG
(CTC)	 AG	72468-72592	GT	AGG
(GAG)	 AG	72731-72922	GT	AGG
(TTT)	 AG	73072-73197	GT	AGG
(AAT)	 AG	73318-73431	GT	AGG
(GCT)	 AG	73611-73757	CC	AAC
-recovered pasa_asmbl_49933.p1, terminal, 73611, 73757
-recovered pasa_asmbl_49933.p1, internal, 72133, 72262
-recovered pasa_asmbl_49933.p1, internal, 72468, 72592
-recovered pasa_asmbl_49933.p1, internal, 72731, 72922
-recovered pasa_asmbl_49933.p1, internal, 73072, 73197
-recovered pasa_asmbl_49933.p1, internal, 73318, 73431
Valid prediction for GlimmerHMM_glimmerT_18412-T1
Valid prediction for GlimmerHMM_glimmerT_18399-T1
Valid prediction for snap_scaffold_7-snap.1981-T1
Valid prediction for snap_scaffold_7-snap.2003-T1
Valid prediction for Augustus_model.g12404.t1
Valid prediction for GeneMark_model.30880_t
Valid prediction for snap_scaffold_7-snap.1972-T1
Valid prediction for GlimmerHMM_glimmerT_18405-T1
Valid prediction for GeneMark_model.30860_t
Valid prediction for snap_scaffold_7-snap.1983-T1
Valid prediction for GlimmerHMM_glimmerT_18404-T1
Valid prediction for GeneMark_model.30845_t
Valid prediction for snap_scaffold_7-snap.1977-T1
Valid prediction for GeneMark_model.30866_t
Valid prediction for snap_scaffold_7-snap.1991-T1
Valid prediction for GeneMark_model.30884_t
Valid prediction for HiQ_model.g12413.t1
Valid prediction for pasa_asmbl_49927.p1
Valid prediction for GlimmerHMM_glimmerT_18417-T1
Valid prediction for snap_scaffold_7-snap.1975-T1
Couldn't classify 225244, 225281
Couldn't classify 225751, 225912
Sorry, prediction pasa_asmbl_49920.p1 fails validation.
(TGC)	 CT	225244-225281	GT	AGG
(AGG)	 AG	225460-225601	GT	TGG
(GTG)	 AG	225751-225912	AG	GCA
-recovered pasa_asmbl_49920.p1, internal, 225460, 225601
Valid prediction for Augustus_model.g12423.t1
Valid prediction for snap_scaffold_7-snap.1969-T1
Valid prediction for GeneMark_model.30852_t
Valid prediction for GeneMark_model.30870_t
Valid prediction for CodingQuarry_transcript_57459-T1
Valid prediction for snap_scaffold_7-snap.1973-T1
Valid prediction for Augustus_model.g12402.t1
Valid prediction for CodingQuarry_transcript_57466-T1
Valid prediction for pasa_asmbl_49929.p1
Valid prediction for GeneMark_model.30859_t
Valid prediction for Augustus_model.g12422.t1
Valid prediction for GeneMark_model.30849_t
Valid prediction for GeneMark_model.30877_t
Valid prediction for GeneMark_model.30865_t
Valid prediction for HiQ_model.g12405.t1
Valid prediction for snap_scaffold_7-snap.2000-T1
Valid prediction for snap_scaffold_7-snap.1979-T1
Valid prediction for GeneMark_model.30876_t
Valid prediction for GlimmerHMM_glimmerT_18414-T1
Valid prediction for pasa_asmbl_49924.p1
Valid prediction for GeneMark_model.30855_t
Valid prediction for Augustus_model.g12400.t1
Valid prediction for snap_scaffold_7-snap.1978-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 40655, rend_intergenic: 29616  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103362, rend_intergenic: 101436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104956, rend_intergenic: 103391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179827, rend_intergenic: 178717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 265112
-exon list size: 629


building trellis

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85.7    
85.9    
86.1    
86.2    
86.4    
86.5    
86.7    
86.8    
87.0    
87.2    
87.3    
87.5    
87.6    
87.8    
88.0    
88.1    
88.3    
88.4    
88.6    
88.7    
88.9    
89.1    
89.2    
89.4    
89.5    
89.7    
89.9    
90.0    
90.2    
90.3    
90.5    
90.6    
90.8    
91.0    
91.1    
91.3    
91.4    
91.6    
91.8    
91.9    
92.1    
92.2    
92.4    
92.6    
92.7    
92.9    
93.0    
93.2    
93.3    
93.5    
93.7    
93.8    
94.0    
94.1    
94.3    
94.5    
94.6    
94.8    
94.9    
95.1    
95.2    
95.4    
95.6    
95.7    
95.9    
96.0    
96.2    
96.4    
96.5    
96.7    
96.8    
97.0    
97.1    
97.3    
97.5    
97.6    
97.8    
97.9    
98.1    
98.3    
98.4    
98.6    
98.7    
98.9    
99.0    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 40655, rend_intergenic: 29616  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103362, rend_intergenic: 101436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104956, rend_intergenic: 103391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179827, rend_intergenic: 178717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 31 predictions persist after filtering for low support