-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_28/scaffold_28_2636393-2781930

-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_28-snap.671-T1
Valid prediction for snap_scaffold_28-snap.680-T1
Valid prediction for Augustus_model.g38668.t1
Valid prediction for snap_scaffold_28-snap.665-T1
Valid prediction for pasa_asmbl_37404.p1
Valid prediction for snap_scaffold_28-snap.684-T1
Valid prediction for snap_scaffold_28-snap.652-T1
Valid prediction for Augustus_model.g38661.t1
Valid prediction for Augustus_model.g38671.t1
Valid prediction for GlimmerHMM_glimmerT_58383-T1
Valid prediction for snap_scaffold_28-snap.673-T1
Valid prediction for snap_scaffold_28-snap.682-T1
Valid prediction for GlimmerHMM_glimmerT_58406-T1
Valid prediction for snap_scaffold_28-snap.670-T1
Valid prediction for snap_scaffold_28-snap.662-T1
Valid prediction for GlimmerHMM_glimmerT_58378-T1
Valid prediction for snap_scaffold_28-snap.656-T1
Valid prediction for CodingQuarry_transcript_43576-T1
Valid prediction for snap_scaffold_28-snap.664-T1
Valid prediction for pasa_asmbl_37407.p1
Valid prediction for HiQ_model.g38676.t1
Valid prediction for snap_scaffold_28-snap.683-T1
Valid prediction for Augustus_model.g38678.t1
Valid prediction for Augustus_model.g38667.t1
Valid prediction for CodingQuarry_transcript_43579-T1
Valid prediction for Augustus_model.g38657.t1
Valid prediction for GlimmerHMM_glimmerT_58392-T1
Valid prediction for CodingQuarry_transcript_43569-T1
Valid prediction for Augustus_model.g38669.t1
Valid prediction for snap_scaffold_28-snap.657-T1
Valid prediction for Augustus_model.g38674.t1
Valid prediction for snap_scaffold_28-snap.669-T1
Valid prediction for GlimmerHMM_glimmerT_58409-T1
Valid prediction for snap_scaffold_28-snap.678-T1
Valid prediction for GlimmerHMM_glimmerT_58390-T1
Valid prediction for snap_scaffold_28-snap.675-T1
Valid prediction for GlimmerHMM_glimmerT_58402-T1
Valid prediction for GlimmerHMM_glimmerT_58391-T1
Valid prediction for pasa_asmbl_37403.p1
Valid prediction for Augustus_model.g38679.t1
Valid prediction for snap_scaffold_28-snap.666-T1
Valid prediction for GlimmerHMM_glimmerT_58384-T1
Valid prediction for CodingQuarry_transcript_43567-T1
Valid prediction for snap_scaffold_28-snap.654-T1
Valid prediction for GlimmerHMM_glimmerT_58380-T1
Valid prediction for GlimmerHMM_glimmerT_58393-T1
Couldn't classify 58841, 59185
Sorry, prediction pasa_asmbl_37400.p1 fails validation.
(CAG)	 CC	58841-59185	AA	GAA
Valid prediction for CodingQuarry_transcript_43568-T1
Valid prediction for pasa_asmbl_37394.p1
Valid prediction for Augustus_model.g38658.t1
Valid prediction for snap_scaffold_28-snap.650-T1
Valid prediction for HiQ_model.g38672.t1
Valid prediction for Augustus_model.g38662.t1
Valid prediction for GlimmerHMM_glimmerT_58397-T1
Couldn't classify 6626, 7293
Sorry, prediction pasa_asmbl_37391.p1 fails validation.
(ATG)	 AC	4796-5006	GT	AGG
(GTC)	 AG	6626-7293	GT	AGG
-recovered pasa_asmbl_37391.p1, initial, 4796, 5006
-recovered pasa_asmbl_37391.p1, internal, 6626, 7293
Valid prediction for snap_scaffold_28-snap.688-T1
Valid prediction for GlimmerHMM_glimmerT_58394-T1
Valid prediction for snap_scaffold_28-snap.660-T1
Valid prediction for snap_scaffold_28-snap.667-T1
Valid prediction for CodingQuarry_transcript_43575-T1
Valid prediction for Augustus_model.g38656.t1
Valid prediction for CodingQuarry_transcript_43578-T1
Valid prediction for Augustus_model.g38666.t1
Valid prediction for CodingQuarry_transcript_43577-T1
Valid prediction for CodingQuarry_transcript_43580-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: -)Couldn't classify 133745, 134173
Sorry, prediction pasa_asmbl_37393.p1 fails validation.
(ATG)	 CC	133745-134173	CT	GCC
Valid prediction for GlimmerHMM_glimmerT_58379-T1
Valid prediction for snap_scaffold_28-snap.686-T1
Valid prediction for snap_scaffold_28-snap.676-T1
Valid prediction for CodingQuarry_transcript_43571-T1
Valid prediction for CodingQuarry_transcript_43574-T1
Valid prediction for snap_scaffold_28-snap.659-T1
Valid prediction for pasa_asmbl_38078.p1
Valid prediction for GlimmerHMM_glimmerT_58395-T1
Valid prediction for GlimmerHMM_glimmerT_58407-T1
Valid prediction for GlimmerHMM_glimmerT_58408-T1
Valid prediction for pasa_asmbl_38070.p1
Valid prediction for GlimmerHMM_glimmerT_58404-T1
Valid prediction for Augustus_model.g38663.t1
Valid prediction for Augustus_model.g38677.t1
Couldn't classify 116329, 116422
Couldn't classify 116893, 117018
Sorry, prediction pasa_asmbl_38074.p1 fails validation.
(CAG)	 CG	116329-116422	GT	AGG
(GTG)	 AG	116602-116732	GT	TGG
(GGT)	 AG	116893-117018	GG	AGG
-recovered pasa_asmbl_38074.p1, internal, 116602, 116732
Couldn't classify 117239, 117279
Sorry, prediction pasa_asmbl_38073.p1 fails validation.
(GTG)	 GG	117239-117279	GT	AGG
(GCT)	 AG	117511-117577	GT	CGG
(GCT)	 AG	117726-118033	GT	AGG
(GTG)	 AG	118147-118187	GT	CGG
(ACG)	 AG	118311-118481	GT	AGG
(GGT)	 AG	118698-118812	GT	GAG
(GGG)	 AG	119048-119162	GG	AAG
add_exon() Sorry, pasa_asmbl_38073.p1 117726-118033-terminal-2 is invalid.
-recovered pasa_asmbl_38073.p1, terminal, 117726, 118033
-recovered pasa_asmbl_38073.p1, terminal, 119048, 119162
-recovered pasa_asmbl_38073.p1, internal, 117511, 117577
-recovered pasa_asmbl_38073.p1, internal, 117726, 118033
-recovered pasa_asmbl_38073.p1, internal, 118147, 118187
-recovered pasa_asmbl_38073.p1, internal, 118311, 118481
-recovered pasa_asmbl_38073.p1, internal, 118698, 118812
Valid prediction for pasa_asmbl_38079.p1
Valid prediction for CodingQuarry_transcript_43573-T1
Valid prediction for GlimmerHMM_glimmerT_58386-T1
Valid prediction for GlimmerHMM_glimmerT_58398-T1
Valid prediction for GlimmerHMM_glimmerT_58388-T1
Valid prediction for GlimmerHMM_glimmerT_58382-T1
Valid prediction for snap_scaffold_28-snap.672-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for HiQ_model.g38665.t1
Valid prediction for GlimmerHMM_glimmerT_58405-T1
Couldn't classify 100364, 100484
Sorry, prediction pasa_asmbl_38558.p1 fails validation.
(GTG)	 CA	100364-100484	GT	CGG
(AGA)	 AG	100746-100823	GT	AGG
(ACG)	 AG	101256-101299	GT	CGG
(AAG)	 AG	102209-102308	GT	AGG
(ATG)	 AG	103332-103440	GT	GGG
(GGA)	 AG	103623-103724	GT	GGG
(CAT)	 AG	103869-103965	GT	AGG
(AGT)	 AG	104098-104209	GT	GGG
(AGC)	 AG	104413-104516	GT	CGG
(GAG)	 AG	104616-104703	GT	AGG
(CTC)	 AG	104884-104999	GT	GGG
(GCC)	 AG	105081-105271	GT	AGG
(GGG)	 AG	105369-105432	GC	GAG
add_exon() Sorry, pasa_asmbl_38558.p1 103332-103440-initial-1 is invalid.
-recovered pasa_asmbl_38558.p1, initial, 103332, 103440
-recovered pasa_asmbl_38558.p1, terminal, 105369, 105432
-recovered pasa_asmbl_38558.p1, internal, 100746, 100823
-recovered pasa_asmbl_38558.p1, internal, 101256, 101299
-recovered pasa_asmbl_38558.p1, internal, 102209, 102308
-recovered pasa_asmbl_38558.p1, internal, 103332, 103440
-recovered pasa_asmbl_38558.p1, internal, 103623, 103724
-recovered pasa_asmbl_38558.p1, internal, 103869, 103965
-recovered pasa_asmbl_38558.p1, internal, 104098, 104209
-recovered pasa_asmbl_38558.p1, internal, 104413, 104516
-recovered pasa_asmbl_38558.p1, internal, 104616, 104703
-recovered pasa_asmbl_38558.p1, internal, 104884, 104999
-recovered pasa_asmbl_38558.p1, internal, 105081, 105271
-recovered pasa_asmbl_38558.p1, internal, 105369, 105432
Valid prediction for GlimmerHMM_glimmerT_58401-T1
Valid prediction for snap_scaffold_28-snap.677-T1
Valid prediction for GlimmerHMM_glimmerT_58385-T1
Valid prediction for CodingQuarry_transcript_43572-T1
Valid prediction for GlimmerHMM_glimmerT_58396-T1
Valid prediction for snap_scaffold_28-snap.679-T1
Valid prediction for GlimmerHMM_glimmerT_58400-T1
Valid prediction for snap_scaffold_28-snap.674-T1
Couldn't classify 7699, 8151
Couldn't classify 8449, 8559
Sorry, prediction pasa_asmbl_38083.p1 fails validation.
(TAT)	 GA	7699-8151	GT	TAG
(GTG)	 AG	8449-8559	TG	CCT
Couldn't classify 48052, 48174
Sorry, prediction pasa_asmbl_38081.p1 fails validation.
(AGC)	 AC	48052-48174	GT	TTG
(GTG)	 AG	48808-48883	GT	AGG
(GCA)	 AG	49200-49369	GC	AGG
(GGC)	 AG	49641-49814	GT	AGG
(GGC)	 AG	50110-50276	GT	GGG
(AAA)	 AG	50584-50884	GT	AGG
(GCT)	 AG	51249-51473	GT	AGG
(ATC)	 AG	51614-51721	GT	AGG
(GTG)	 AG	51830-51974	GT	CTG
(GCC)	 AG	52086-52236	GT	AGG
(GAA)	 AG	52565-52643	AG	AAA
-recovered pasa_asmbl_38081.p1, terminal, 52565, 52643
-recovered pasa_asmbl_38081.p1, internal, 48808, 48883
-recovered pasa_asmbl_38081.p1, internal, 49200, 49369
-recovered pasa_asmbl_38081.p1, internal, 49641, 49814
-recovered pasa_asmbl_38081.p1, internal, 50110, 50276
-recovered pasa_asmbl_38081.p1, internal, 50584, 50884
-recovered pasa_asmbl_38081.p1, internal, 51249, 51473
-recovered pasa_asmbl_38081.p1, internal, 51614, 51721
-recovered pasa_asmbl_38081.p1, internal, 51830, 51974
-recovered pasa_asmbl_38081.p1, internal, 52086, 52236
Valid prediction for snap_scaffold_28-snap.681-T1
Valid prediction for snap_scaffold_28-snap.687-T1
Valid prediction for snap_scaffold_28-snap.661-T1
Valid prediction for GlimmerHMM_glimmerT_58389-T1
Valid prediction for snap_scaffold_28-snap.685-T1
Valid prediction for snap_scaffold_28-snap.653-T1
Valid prediction for HiQ_model.g38659.t1
Valid prediction for HiQ_model.g38673.t1
Valid prediction for GlimmerHMM_glimmerT_58403-T1
Valid prediction for GlimmerHMM_glimmerT_58399-T1
Valid prediction for GlimmerHMM_glimmerT_58381-T1
Valid prediction for snap_scaffold_28-snap.651-T1
Valid prediction for snap_scaffold_28-snap.663-T1
Valid prediction for snap_scaffold_28-snap.668-T1
Valid prediction for snap_scaffold_28-snap.649-T1
Valid prediction for snap_scaffold_28-snap.658-T1
Valid prediction for Augustus_model.g38675.t1
Valid prediction for CodingQuarry_transcript_43570-T1
Valid prediction for GlimmerHMM_glimmerT_58387-T1
Valid prediction for snap_scaffold_28-snap.655-T1
Couldn't classify 114892, 114990
Couldn't classify 115659, 115831
Sorry, prediction pasa_asmbl_38552.p1 fails validation.
(TCG)	 TC	114892-114990	GT	AGG
(CAA)	 AG	115155-115242	GT	AGG
(GCG)	 AG	115343-115468	GT	AGG
(GTG)	 AG	115659-115831	AT	ACA
-recovered pasa_asmbl_38552.p1, internal, 115155, 115242
-recovered pasa_asmbl_38552.p1, internal, 115343, 115468
Valid prediction for Augustus_model.g38670.t1
Valid prediction for Augustus_model.g38660.t1
Valid prediction for HiQ_model.g38664.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11109, rend_intergenic: 4796  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15242, rend_intergenic: 12736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18517, rend_intergenic: 16072  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20637, rend_intergenic: 19361  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29815, rend_intergenic: 26377  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30558, rend_intergenic: 30391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37522, rend_intergenic: 35974  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48065, rend_intergenic: 40232  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53841, rend_intergenic: 48856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74443, rend_intergenic: 69406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83236, rend_intergenic: 79671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88827, rend_intergenic: 87096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90619, rend_intergenic: 89108  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105382, rend_intergenic: 101738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126544, rend_intergenic: 119240  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 145538
-exon list size: 504


building trellis

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94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 11109, rend_intergenic: 4796  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15242, rend_intergenic: 12736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18517, rend_intergenic: 16072  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20637, rend_intergenic: 19361  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29815, rend_intergenic: 26377  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30558, rend_intergenic: 30391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37522, rend_intergenic: 35974  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48065, rend_intergenic: 40232  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53841, rend_intergenic: 48856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74443, rend_intergenic: 69406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83236, rend_intergenic: 79671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88827, rend_intergenic: 87096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90619, rend_intergenic: 89108  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105382, rend_intergenic: 101738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126544, rend_intergenic: 119240  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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