-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_13/scaffold_13_14985949-15247735

-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_32884-T1
Valid prediction for snap_scaffold_13-snap.2924-T1
Valid prediction for HiQ_model.g21935.t1
Valid prediction for GlimmerHMM_glimmerT_32859-T1
Valid prediction for snap_scaffold_13-snap.2921-T1
Valid prediction for HiQ_model.g21923.t1
Valid prediction for GlimmerHMM_glimmerT_32866-T1
Couldn't classify 67103, 67132
Couldn't classify 67384, 67890
Sorry, prediction pasa_asmbl_11481.p1 fails validation.
(AGG)	 GG	67103-67132	GT	AGG
(GCT)	 AG	67384-67890	AC	CCA
Valid prediction for snap_scaffold_13-snap.2930-T1
Valid prediction for snap_scaffold_13-snap.2944-T1
Valid prediction for GlimmerHMM_glimmerT_32871-T1
Valid prediction for GlimmerHMM_glimmerT_32856-T1
Valid prediction for snap_scaffold_13-snap.2906-T1
Valid prediction for GlimmerHMM_glimmerT_32858-T1
Valid prediction for snap_scaffold_13-snap.2939-T1
Valid prediction for GlimmerHMM_glimmerT_32854-T1
Valid prediction for Augustus_model.g21934.t1
Valid prediction for snap_scaffold_13-snap.2907-T1
Valid prediction for GlimmerHMM_glimmerT_32869-T1
Valid prediction for GlimmerHMM_glimmerT_32865-T1
Valid prediction for snap_scaffold_13-snap.2901-T1
Valid prediction for GlimmerHMM_glimmerT_32862-T1
Couldn't classify 110591, 110764
Sorry, prediction pasa_asmbl_11485.p1 fails validation.
(TCC)	 CC	110591-110764	GT	TGG
(GAC)	 AG	111468-111565	GT	AGG
(GGG)	 AG	111981-112044	GT	CTG
(ATG)	 AG	112637-112780	GT	AGG
(GGT)	 AG	114119-114202	GT	AGG
(GTG)	 AG	114477-114630	GT	AGG
(GGG)	 AG	116356-116465	AT	AGA
-recovered pasa_asmbl_11485.p1, initial, 112637, 112780
-recovered pasa_asmbl_11485.p1, terminal, 116356, 116465
-recovered pasa_asmbl_11485.p1, internal, 111468, 111565
-recovered pasa_asmbl_11485.p1, internal, 111981, 112044
-recovered pasa_asmbl_11485.p1, internal, 112637, 112780
-recovered pasa_asmbl_11485.p1, internal, 114119, 114202
-recovered pasa_asmbl_11485.p1, internal, 114477, 114630
Valid prediction for GlimmerHMM_glimmerT_32878-T1
Valid prediction for GlimmerHMM_glimmerT_32874-T1
Valid prediction for snap_scaffold_13-snap.2902-T1
Valid prediction for GlimmerHMM_glimmerT_32888-T1
Valid prediction for snap_scaffold_13-snap.2894-T1
Valid prediction for snap_scaffold_13-snap.2928-T1
Valid prediction for snap_scaffold_13-snap.2943-T1
Valid prediction for snap_scaffold_13-snap.2895-T1
Valid prediction for Augustus_model.g21925.t1
Valid prediction for pasa_asmbl_11489.p1
Couldn't classify 99256, 99521
Sorry, prediction pasa_asmbl_11483.p1 fails validation.
(ATG)	 AC	96945-97050	GT	CGG
(CCC)	 AG	99256-99521	CA	ACC
-recovered pasa_asmbl_11483.p1, initial, 96945, 97050
Valid prediction for snap_scaffold_13-snap.2908-T1
Valid prediction for GlimmerHMM_glimmerT_32863-T1
Valid prediction for snap_scaffold_13-snap.2935-T1
Valid prediction for snap_scaffold_13-snap.2926-T1
Valid prediction for snap_scaffold_13-snap.2897-T1
Valid prediction for snap_scaffold_13-snap.2941-T1
Valid prediction for CodingQuarry_transcript_13325-T1
Valid prediction for snap_scaffold_13-snap.2900-T1
Valid prediction for Augustus_model.g21921.t1
Valid prediction for GlimmerHMM_glimmerT_32861-T1
Valid prediction for HiQ_model.g21927.t1
Valid prediction for snap_scaffold_13-snap.2904-T1
Valid prediction for GlimmerHMM_glimmerT_32870-T1
Valid prediction for Augustus_model.g21917.t1
Couldn't classify 68899, 68941
Couldn't classify 70429, 70527
Sorry, prediction pasa_asmbl_11590.p1 fails validation.
(CTG)	 CG	68899-68941	GT	GGG
(ACA)	 AG	69925-70103	GT	AGG
(GAG)	 AG	70429-70527	TC	GGT
-recovered pasa_asmbl_11590.p1, internal, 69925, 70103
Valid prediction for snap_scaffold_13-snap.2947-T1
Valid prediction for pasa_asmbl_11480.p1
Valid prediction for Augustus_model.g21919.t1
Valid prediction for GlimmerHMM_glimmerT_32885-T1
Valid prediction for Augustus_model.g21924.t1
Valid prediction for snap_scaffold_13-snap.2946-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_13-snap.2896-T1
Valid prediction for snap_scaffold_13-snap.2916-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_13-snap.2915-T1
Valid prediction for snap_scaffold_13-snap.2911-T1
Valid prediction for GlimmerHMM_glimmerT_32887-T1
Couldn't classify 105168, 105293
Couldn't classify 106672, 106704
Sorry, prediction pasa_asmbl_11484.p1 fails validation.
(ACG)	 AG	105168-105293	GT	AGG
(ACG)	 AG	106051-106212	GT	TGG
(GGC)	 AG	106672-106704	TG	TGT
-recovered pasa_asmbl_11484.p1, internal, 105168, 105293
-recovered pasa_asmbl_11484.p1, internal, 106051, 106212
Valid prediction for snap_scaffold_13-snap.2938-T1
Valid prediction for GlimmerHMM_glimmerT_32868-T1
Valid prediction for snap_scaffold_13-snap.2912-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_13-snap.2923-T1
Valid prediction for snap_scaffold_13-snap.2927-T1
Valid prediction for snap_scaffold_13-snap.2931-T1
Valid prediction for snap_scaffold_13-snap.2929-T1
Valid prediction for GlimmerHMM_glimmerT_32881-T1
Valid prediction for snap_scaffold_13-snap.2910-T1
Couldn't classify 1652, 1797
Sorry, prediction pasa_asmbl_10234.p1 fails validation.
(CGT)	 GA	1652-1797	GT	AGG
(AAT)	 AG	2497-2598	GT	GTG
(CGA)	 AG	2733-2964	TG	AAT
-recovered pasa_asmbl_10234.p1, terminal, 2733, 2964
-recovered pasa_asmbl_10234.p1, internal, 2497, 2598
Valid prediction for snap_scaffold_13-snap.2922-T1
Valid prediction for snap_scaffold_13-snap.2933-T1
Valid prediction for Augustus_model.g21933.t1
Valid prediction for snap_scaffold_13-snap.2936-T1
Valid prediction for Augustus_model.g21928.t1
Valid prediction for Augustus_model.g21916.t1
Valid prediction for GlimmerHMM_glimmerT_32877-T1
Valid prediction for Augustus_model.g21931.t1
Valid prediction for GlimmerHMM_glimmerT_32855-T1
Valid prediction for snap_scaffold_13-snap.2918-T1
Valid prediction for GlimmerHMM_glimmerT_32880-T1
Valid prediction for snap_scaffold_13-snap.2934-T1
Valid prediction for GlimmerHMM_glimmerT_32867-T1
Valid prediction for snap_scaffold_13-snap.2932-T1
Valid prediction for Augustus_model.g21920.t1
Valid prediction for Augustus_model.g21929.t1
Valid prediction for GlimmerHMM_glimmerT_32864-T1
Couldn't classify 54332, 54402
Sorry, prediction pasa_asmbl_10344.p1 fails validation.
(ATG)	 TC	49224-49390	GT	CTG
(GCG)	 AG	50900-50993	GT	AGG
(GTG)	 AG	52497-52612	GT	TGG
(GTA)	 AG	52952-53090	GT	AGG
(TCT)	 AG	53559-53715	GT	AGG
(CAA)	 AG	54332-54402	CC	CTC
-recovered pasa_asmbl_10344.p1, initial, 49224, 49390
-recovered pasa_asmbl_10344.p1, internal, 50900, 50993
-recovered pasa_asmbl_10344.p1, internal, 52497, 52612
-recovered pasa_asmbl_10344.p1, internal, 52952, 53090
-recovered pasa_asmbl_10344.p1, internal, 53559, 53715
Valid prediction for GlimmerHMM_glimmerT_32882-T1
Valid prediction for snap_scaffold_13-snap.2920-T1
Valid prediction for snap_scaffold_13-snap.2940-T1
Couldn't classify 180127, 180344
Sorry, prediction pasa_asmbl_10226.p1 fails validation.
(ATG)	 GT	170266-170311	GT	AGG
(ATC)	 AG	170603-170693	GT	AAG
(TTT)	 AG	171282-171357	GT	AGG
(TCG)	 AG	172219-172311	GT	CTG
(GTG)	 AG	173774-173853	GT	AGG
(GGA)	 AG	176292-176358	GT	AGG
(GCC)	 AG	177398-177460	GT	AGG
(AGG)	 AG	179447-179534	GT	CGG
(GCT)	 AG	180127-180344	TT	CGT
-recovered pasa_asmbl_10226.p1, initial, 170266, 170311
-recovered pasa_asmbl_10226.p1, internal, 170603, 170693
-recovered pasa_asmbl_10226.p1, internal, 171282, 171357
-recovered pasa_asmbl_10226.p1, internal, 172219, 172311
-recovered pasa_asmbl_10226.p1, internal, 173774, 173853
-recovered pasa_asmbl_10226.p1, internal, 176292, 176358
-recovered pasa_asmbl_10226.p1, internal, 177398, 177460
-recovered pasa_asmbl_10226.p1, internal, 179447, 179534
Valid prediction for snap_scaffold_13-snap.2945-T1
Valid prediction for snap_scaffold_13-snap.2949-T1
Valid prediction for GlimmerHMM_glimmerT_32889-T1
Valid prediction for GlimmerHMM_glimmerT_32873-T1
Valid prediction for Augustus_model.g21918.t1
Valid prediction for Augustus_model.g21915.t1
Valid prediction for GlimmerHMM_glimmerT_32876-T1
Valid prediction for snap_scaffold_13-snap.2913-T1
Valid prediction for GlimmerHMM_glimmerT_32886-T1
Valid prediction for GlimmerHMM_glimmerT_32872-T1
Couldn't classify 59145, 59295
Sorry, prediction pasa_asmbl_10228.p2 fails validation.
(TTC)	 TC	59145-59295	GT	TGG
(GTC)	 AG	59559-59653	GT	TGG
(GCG)	 AG	60251-60310	CG	AGC
-recovered pasa_asmbl_10228.p2, terminal, 60251, 60310
-recovered pasa_asmbl_10228.p2, internal, 59559, 59653
Couldn't classify 45678, 45734
Couldn't classify 47569, 47686
Sorry, prediction pasa_asmbl_10231.p1 fails validation.
(GTG)	 AG	45678-45734	GT	AGG
(TTT)	 AG	46059-46190	GT	AGG
(ACC)	 AG	46526-46671	GT	AAG
(AGA)	 AG	47569-47686	GA	AAG
-recovered pasa_asmbl_10231.p1, internal, 45678, 45734
-recovered pasa_asmbl_10231.p1, internal, 46059, 46190
-recovered pasa_asmbl_10231.p1, internal, 46526, 46671
Valid prediction for snap_scaffold_13-snap.2909-T1
Valid prediction for Augustus_model.g21932.t1
Valid prediction for snap_scaffold_13-snap.2925-T1
Valid prediction for GlimmerHMM_glimmerT_32883-T1
Valid prediction for snap_scaffold_13-snap.2919-T1
Valid prediction for snap_scaffold_13-snap.2937-T1
Valid prediction for GlimmerHMM_glimmerT_32860-T1
Valid prediction for snap_scaffold_13-snap.2903-T1
Valid prediction for GlimmerHMM_glimmerT_32875-T1
Valid prediction for GlimmerHMM_glimmerT_32879-T1
Valid prediction for snap_scaffold_13-snap.2948-T1
Valid prediction for snap_scaffold_13-snap.2899-T1
Valid prediction for Augustus_model.g21926.t1
Valid prediction for snap_scaffold_13-snap.2914-T1
Valid prediction for HiQ_model.g21936.t1
Valid prediction for GlimmerHMM_glimmerT_32857-T1
Valid prediction for snap_scaffold_13-snap.2905-T1
Couldn't classify 255110, 255233
Sorry, prediction pasa_asmbl_10221.p1 fails validation.
(ATG)	 AC	249220-249540	GT	AGG
(GTG)	 AG	251447-251578	GT	GGG
(ACC)	 AG	251903-252002	GT	AGG
(ATT)	 AG	252708-252852	GT	AAG
(ATG)	 AG	255110-255233	AA	AGA
-recovered pasa_asmbl_10221.p1, initial, 249220, 249540
-recovered pasa_asmbl_10221.p1, internal, 251447, 251578
-recovered pasa_asmbl_10221.p1, internal, 251903, 252002
-recovered pasa_asmbl_10221.p1, internal, 252708, 252852
Valid prediction for Augustus_model.g21930.t1
Valid prediction for Augustus_model.g21914.t1
Valid prediction for HiQ_model.g21922.t1
Couldn't classify 207447, 207583
Sorry, prediction pasa_asmbl_10222.p1 fails validation.
(AAA)	 GG	207447-207583	GT	AGG
(GTG)	 AG	208214-208369	GT	AGG
(CCC)	 AG	210300-210348	GG	AAG
-recovered pasa_asmbl_10222.p1, terminal, 210300, 210348
-recovered pasa_asmbl_10222.p1, internal, 208214, 208369
Valid prediction for snap_scaffold_13-snap.2898-T1
Valid prediction for snap_scaffold_13-snap.2917-T1
Couldn't classify 212280, 212761
Sorry, prediction CodingQuarry_transcript_13324-T1 fails validation.
(ATG)	 TC	212280-212761	AG	AGA
(TGA)	 AG	212788-212812	GA	GAG
-recovered CodingQuarry_transcript_13324-T1, terminal, 212788, 212812
Valid prediction for CodingQuarry_transcript_13327-T1
Valid prediction for snap_scaffold_13-snap.2942-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18813, rend_intergenic: 15677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27161, rend_intergenic: 23412  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35803, rend_intergenic: 28301  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50708, rend_intergenic: 36599  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60029, rend_intergenic: 51471  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69315, rend_intergenic: 61511  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70211, rend_intergenic: 69764  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85317, rend_intergenic: 78165  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91522, rend_intergenic: 85485  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112152, rend_intergenic: 97570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117222, rend_intergenic: 112675  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134950, rend_intergenic: 128861  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136500, rend_intergenic: 134979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147208, rend_intergenic: 146938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183042, rend_intergenic: 182729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188190, rend_intergenic: 183073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195207, rend_intergenic: 193045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198268, rend_intergenic: 196189  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206691, rend_intergenic: 201478  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211172, rend_intergenic: 208147  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 217690, rend_intergenic: 212997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 247261, rend_intergenic: 217853  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 261787
-exon list size: 454


building trellis

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75.7    
75.9    
76.1    
76.3    
76.5    
76.8    
77.0    
77.2    
77.4    
77.6    
77.9    
78.1    
78.3    
78.5    
78.7    
78.9    
79.2    
79.4    
79.6    
79.8    
80.0    
80.3    
80.5    
80.7    
80.9    
81.1    
81.4    
81.6    
81.8    
82.0    
82.2    
82.5    
82.7    
82.9    
83.1    
83.3    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.9    
85.1    
85.3    
85.5    
85.7    
86.0    
86.2    
86.4    
86.6    
86.8    
87.1    
87.3    
87.5    
87.7    
87.9    
88.2    
88.4    
88.6    
88.8    
89.0    
89.3    
89.5    
89.7    
89.9    
90.1    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.7    
91.9    
92.1    
92.3    
92.5    
92.8    
93.0    
93.2    
93.4    
93.6    
93.9    
94.1    
94.3    
94.5    
94.7    
95.0    
95.2    
95.4    
95.6    
95.8    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.4    
97.6    
97.8    
98.0    
98.2    
98.5    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 18813, rend_intergenic: 15677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27161, rend_intergenic: 23412  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35803, rend_intergenic: 28301  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50708, rend_intergenic: 36599  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60029, rend_intergenic: 51471  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69315, rend_intergenic: 61511  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70211, rend_intergenic: 69764  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85317, rend_intergenic: 78165  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91522, rend_intergenic: 85485  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112152, rend_intergenic: 97570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117222, rend_intergenic: 112675  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134950, rend_intergenic: 128861  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136500, rend_intergenic: 134979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147208, rend_intergenic: 146938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183042, rend_intergenic: 182729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188190, rend_intergenic: 183073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195207, rend_intergenic: 193045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198268, rend_intergenic: 196189  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206691, rend_intergenic: 201478  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211172, rend_intergenic: 208147  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 217690, rend_intergenic: 212997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 247261, rend_intergenic: 217853  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support