-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_15/scaffold_15_13922115-14117821

-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_15-snap.2786-T1
Valid prediction for Augustus_model.g24864.t1
Valid prediction for GlimmerHMM_glimmerT_37302-T1
Valid prediction for snap_scaffold_15-snap.2814-T1
Valid prediction for snap_scaffold_15-snap.2799-T1
Valid prediction for GlimmerHMM_glimmerT_37324-T1
Valid prediction for GlimmerHMM_glimmerT_37328-T1
Valid prediction for snap_scaffold_15-snap.2793-T1
Valid prediction for pasa_asmbl_15667.p1
Valid prediction for Augustus_model.g24879.t1
Valid prediction for Augustus_model.g24873.t1
Valid prediction for Augustus_model.g24854.t1
Valid prediction for GlimmerHMM_glimmerT_37310-T1
Valid prediction for snap_scaffold_15-snap.2805-T1
Valid prediction for GlimmerHMM_glimmerT_37325-T1
Valid prediction for GlimmerHMM_glimmerT_37332-T1
Valid prediction for snap_scaffold_15-snap.2789-T1
Valid prediction for GlimmerHMM_glimmerT_37320-T1
Valid prediction for HiQ_model.g24872.t1
Valid prediction for HiQ_model.g24859.t1
Valid prediction for snap_scaffold_15-snap.2810-T1
Valid prediction for Augustus_model.g24868.t1
Valid prediction for snap_scaffold_15-snap.2798-T1
Valid prediction for Augustus_model.g24877.t1
Valid prediction for snap_scaffold_15-snap.2806-T1
Valid prediction for snap_scaffold_15-snap.2821-T1
Valid prediction for CodingQuarry_transcript_18220-T1
Valid prediction for snap_scaffold_15-snap.2788-T1
Valid prediction for GlimmerHMM_glimmerT_37315-T1
Valid prediction for pasa_asmbl_15666.p1
Valid prediction for Augustus_model.g24880.t1
Valid prediction for GlimmerHMM_glimmerT_37326-T1
Valid prediction for Augustus_model.g24870.t1
Valid prediction for GlimmerHMM_glimmerT_37303-T1
Valid prediction for snap_scaffold_15-snap.2779-T1
Valid prediction for snap_scaffold_15-snap.2809-T1
Valid prediction for pasa_asmbl_15659.p1
Valid prediction for CodingQuarry_transcript_18218-T1
Valid prediction for GlimmerHMM_glimmerT_37333-T1
Valid prediction for snap_scaffold_15-snap.2803-T1
Couldn't classify 4889, 4938
Sorry, prediction pasa_asmbl_15658.p1 fails validation.
(CAG)	 GC	4889-4938	GT	GCG
(TCT)	 AG	5130-5248	GT	TGG
(CTG)	 AG	5576-5738	GT	AAG
(AGA)	 AG	5831-5955	GT	AGG
(ATG)	 AG	6188-6347	GT	GCG
(CGA)	 AG	6620-6795	GT	AGG
(ACT)	 AG	7075-7223	GT	ACG
(AGC)	 AG	7419-7512	GT	TGG
(GCC)	 AG	7743-7854	GT	AAG
(CAC)	 AG	7943-8017	GT	AGG
(GTC)	 AG	8363-8503	GT	AGG
(TCC)	 AG	8640-8746	GT	AGG
(GTA)	 AG	8925-9070	GT	AGG
(GGT)	 AG	9374-9535	CT	AGC
add_exon() Sorry, pasa_asmbl_15658.p1 6188-6347-initial-1 is invalid.
-recovered pasa_asmbl_15658.p1, initial, 6188, 6347
-recovered pasa_asmbl_15658.p1, terminal, 9374, 9535
-recovered pasa_asmbl_15658.p1, internal, 5130, 5248
-recovered pasa_asmbl_15658.p1, internal, 5576, 5738
-recovered pasa_asmbl_15658.p1, internal, 5831, 5955
-recovered pasa_asmbl_15658.p1, internal, 6188, 6347
-recovered pasa_asmbl_15658.p1, internal, 6620, 6795
-recovered pasa_asmbl_15658.p1, internal, 7075, 7223
-recovered pasa_asmbl_15658.p1, internal, 7419, 7512
-recovered pasa_asmbl_15658.p1, internal, 7743, 7854
-recovered pasa_asmbl_15658.p1, internal, 7943, 8017
-recovered pasa_asmbl_15658.p1, internal, 8363, 8503
-recovered pasa_asmbl_15658.p1, internal, 8640, 8746
-recovered pasa_asmbl_15658.p1, internal, 8925, 9070
Valid prediction for pasa_asmbl_15660.p1
Valid prediction for GlimmerHMM_glimmerT_37322-T1
Valid prediction for snap_scaffold_15-snap.2784-T1
Valid prediction for snap_scaffold_15-snap.2780-T1
Valid prediction for snap_scaffold_15-snap.2816-T1
Valid prediction for HiQ_model.g24860.t1
Valid prediction for Augustus_model.g24869.t1
Valid prediction for GlimmerHMM_glimmerT_37309-T1
Valid prediction for GlimmerHMM_glimmerT_37319-T1
Valid prediction for snap_scaffold_15-snap.2820-T1
Valid prediction for HiQ_model.g24867.t1
Valid prediction for GlimmerHMM_glimmerT_37330-T1
Valid prediction for snap_scaffold_15-snap.2792-T1
Valid prediction for GlimmerHMM_glimmerT_37316-T1
Valid prediction for snap_scaffold_15-snap.2796-T1
Valid prediction for CodingQuarry_transcript_18214-T1
Valid prediction for snap_scaffold_15-snap.2818-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 GlimmerHMM_glimmerT_37308-T1
Valid prediction for GlimmerHMM_glimmerT_37306-T1
Valid prediction for snap_scaffold_15-snap.2794-T1
Valid prediction for snap_scaffold_15-snap.2815-T1
Valid prediction for GlimmerHMM_glimmerT_37307-T1
Valid prediction for snap_scaffold_15-snap.2800-T1
Valid prediction for GlimmerHMM_glimmerT_37314-T1
Valid prediction for snap_scaffold_15-snap.2812-T1
Valid prediction for GlimmerHMM_glimmerT_37313-T1
Valid prediction for GlimmerHMM_glimmerT_37321-T1
Valid prediction for HiQ_model.g24861.t1
Valid prediction for Augustus_model.g24858.t1
Valid prediction for Augustus_model.g24863.t1
Valid prediction for snap_scaffold_15-snap.2781-T1
Valid prediction for snap_scaffold_15-snap.2787-T1
Couldn't classify 131818, 131856
Couldn't classify 133389, 133504
Sorry, prediction pasa_asmbl_14696.p2 fails validation.
(CAC)	 AC	131818-131856	GT	AGG
(CGG)	 AG	132764-132938	GT	AGG
(AGT)	 AG	133389-133504	GA	TAG
-recovered pasa_asmbl_14696.p2, internal, 132764, 132938
Valid prediction for snap_scaffold_15-snap.2790-T1
Valid prediction for snap_scaffold_15-snap.2817-T1
Valid prediction for snap_scaffold_15-snap.2813-T1
Valid prediction for pasa_asmbl_14699.p1
Valid prediction for snap_scaffold_15-snap.2782-T1
Valid prediction for snap_scaffold_15-snap.2811-T1
Valid prediction for pasa_asmbl_14692.p2
Valid prediction for snap_scaffold_15-snap.2791-T1
Couldn't classify 115427, 115546
Sorry, prediction pasa_asmbl_14700.p1 fails validation.
(ATG)	 TA	114470-114789	GT	CTG
(ATG)	 AG	114921-115020	GT	AGG
(ACA)	 AG	115427-115546	AA	CGA
-recovered pasa_asmbl_14700.p1, initial, 114470, 114789
-recovered pasa_asmbl_14700.p1, initial, 114921, 115020
-recovered pasa_asmbl_14700.p1, internal, 114921, 115020
Valid prediction for Augustus_model.g24874.t1
Valid prediction for CodingQuarry_transcript_18219-T1
Valid prediction for snap_scaffold_15-snap.2785-T1
Couldn't classify 119785, 120204
Sorry, prediction pasa_asmbl_14697.p1 fails validation.
(TCC)	 AG	119785-120204	GT	TGG
(GTG)	 AG	120762-121043	GA	GAG
-recovered pasa_asmbl_14697.p1, terminal, 120762, 121043
-recovered pasa_asmbl_14697.p1, internal, 119785, 120204
Valid prediction for snap_scaffold_15-snap.2801-T1
Valid prediction for GlimmerHMM_glimmerT_37311-T1
Valid prediction for snap_scaffold_15-snap.2804-T1
Valid prediction for GlimmerHMM_glimmerT_37304-T1
Valid prediction for GlimmerHMM_glimmerT_37318-T1
Couldn't classify 155705, 155770
Couldn't classify 157309, 157446
Sorry, prediction pasa_asmbl_14690.p2 fails validation.
(GTC)	 GT	155705-155770	GT	AGG
(GTC)	 AG	156193-156325	GT	GAG
(ACC)	 AG	156413-156524	GT	AGG
(GCT)	 AG	156998-157103	GT	AGG
(GGC)	 AG	157309-157446	CT	ACC
add_exon() Sorry, pasa_asmbl_14690.p2 156193-156325-terminal-3 is invalid.
-recovered pasa_asmbl_14690.p2, terminal, 156193, 156325
-recovered pasa_asmbl_14690.p2, internal, 156193, 156325
-recovered pasa_asmbl_14690.p2, internal, 156413, 156524
-recovered pasa_asmbl_14690.p2, internal, 156998, 157103
Couldn't classify 165710, 165805
Sorry, prediction pasa_asmbl_14682.p1 fails validation.
(CAG)	 AC	165710-165805	GT	CGG
(GGG)	 AG	165988-166091	GT	AAG
(CGA)	 AG	166274-166404	GT	TGG
(GCT)	 AG	166520-166716	GT	TGG
(GAC)	 AG	166952-167078	GT	TGG
(GTC)	 AG	167186-167317	GT	AGG
(GTG)	 AG	167642-167913	GT	AGG
(GTT)	 AG	168433-168645	GT	TAG
(GAC)	 AG	168918-169067	GT	TGG
(GGC)	 AG	169174-169540	GT	AGG
(TGA)	 AG	170024-170176	GT	AGG
(TCT)	 AG	170420-170654	GT	TCG
(GTA)	 AG	170957-171093	GT	TGG
(ATG)	 AG	171498-171615	GT	AGG
(CAT)	 AG	171982-172128	GT	AAG
(GCT)	 AG	172494-172678	GT	AGG
(GTG)	 AG	172996-173182	GT	ATG
(ATC)	 AG	173298-173450	GT	AGG
(GGA)	 AG	173790-173859	GT	AGG
(GTG)	 AG	174006-174434	GG	GAG
add_exon() Sorry, pasa_asmbl_14682.p1 171498-171615-initial-1 is invalid.
-recovered pasa_asmbl_14682.p1, initial, 171498, 171615
-recovered pasa_asmbl_14682.p1, terminal, 174006, 174434
-recovered pasa_asmbl_14682.p1, internal, 165988, 166091
-recovered pasa_asmbl_14682.p1, internal, 166274, 166404
-recovered pasa_asmbl_14682.p1, internal, 166520, 166716
-recovered pasa_asmbl_14682.p1, internal, 166952, 167078
-recovered pasa_asmbl_14682.p1, internal, 167186, 167317
-recovered pasa_asmbl_14682.p1, internal, 167642, 167913
-recovered pasa_asmbl_14682.p1, internal, 168433, 168645
-recovered pasa_asmbl_14682.p1, internal, 168918, 169067
-recovered pasa_asmbl_14682.p1, internal, 169174, 169540
-recovered pasa_asmbl_14682.p1, internal, 170024, 170176
-recovered pasa_asmbl_14682.p1, internal, 170420, 170654
-recovered pasa_asmbl_14682.p1, internal, 170957, 171093
-recovered pasa_asmbl_14682.p1, internal, 171498, 171615
-recovered pasa_asmbl_14682.p1, internal, 171982, 172128
-recovered pasa_asmbl_14682.p1, internal, 172494, 172678
-recovered pasa_asmbl_14682.p1, internal, 172996, 173182
-recovered pasa_asmbl_14682.p1, internal, 173298, 173450
-recovered pasa_asmbl_14682.p1, internal, 173790, 173859
Couldn't classify 173740, 173859
Sorry, prediction pasa_asmbl_14681.p1 fails validation.
(TGT)	 CG	173740-173859	GT	AGG
(GTG)	 AG	174006-174434	GG	GAG
-recovered pasa_asmbl_14681.p1, terminal, 174006, 174434
Valid prediction for pasa_asmbl_14701.p1
Valid prediction for CodingQuarry_transcript_18216-T1
Valid prediction for snap_scaffold_15-snap.2819-T1
Valid prediction for HiQ_model.g24871.t1
Valid prediction for Augustus_model.g24878.t1
Valid prediction for Augustus_model.g24876.t1
Couldn't classify 163123, 163231
Couldn't classify 164042, 164139
Sorry, prediction pasa_asmbl_14687.p2 fails validation.
(CTG)	 AG	163123-163231	GT	AGG
(GGA)	 AG	163453-163626	GT	CGG
(ATT)	 AG	164042-164139	TC	GCT
-recovered pasa_asmbl_14687.p2, internal, 163123, 163231
-recovered pasa_asmbl_14687.p2, internal, 163453, 163626
Couldn't classify 134851, 134936
Sorry, prediction pasa_asmbl_14693.p1 fails validation.
(AGG)	 CT	134851-134936	GT	GGG
(GGC)	 AG	135045-135129	GT	AGG
(TTC)	 AG	135449-135555	GT	AGG
(AGT)	 AG	136413-136548	GT	GGG
(GAT)	 AG	136902-136981	GT	AGG
(CGT)	 AG	137189-137267	GT	AGG
(CTG)	 AG	137500-137579	GT	AGG
(TTT)	 AG	137745-137859	CA	AAC
-recovered pasa_asmbl_14693.p1, terminal, 137745, 137859
-recovered pasa_asmbl_14693.p1, internal, 135045, 135129
-recovered pasa_asmbl_14693.p1, internal, 135449, 135555
-recovered pasa_asmbl_14693.p1, internal, 136413, 136548
-recovered pasa_asmbl_14693.p1, internal, 136902, 136981
-recovered pasa_asmbl_14693.p1, internal, 137189, 137267
-recovered pasa_asmbl_14693.p1, internal, 137500, 137579
Valid prediction for GlimmerHMM_glimmerT_37312-T1
Valid prediction for GlimmerHMM_glimmerT_37323-T1
Valid prediction for GlimmerHMM_glimmerT_37329-T1
Valid prediction for snap_scaffold_15-snap.2797-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_15-snap.2807-T1
Valid prediction for Augustus_model.g24856.t1
Valid prediction for Augustus_model.g24866.t1
Valid prediction for snap_scaffold_15-snap.2808-T1
Valid prediction for GlimmerHMM_glimmerT_37317-T1
Valid prediction for snap_scaffold_15-snap.2795-T1
Couldn't classify 160462, 160582
Couldn't classify 161162, 161252
Sorry, prediction pasa_asmbl_14689.p1 fails validation.
(CCC)	 CC	160462-160582	GT	CGG
(GTA)	 AG	160766-160916	GT	AGG
(TGA)	 AG	161162-161252	TA	AGT
-recovered pasa_asmbl_14689.p1, internal, 160766, 160916
Valid prediction for GlimmerHMM_glimmerT_37305-T1
Valid prediction for snap_scaffold_15-snap.2802-T1
Valid prediction for Augustus_model.g24855.t1
Valid prediction for Augustus_model.g24875.t1
Valid prediction for HiQ_model.g24862.t1
Valid prediction for GlimmerHMM_glimmerT_37327-T1
Valid prediction for GlimmerHMM_glimmerT_37331-T1
Valid prediction for HiQ_model.g24865.t1
Valid prediction for snap_scaffold_15-snap.2783-T1
Couldn't classify 164514, 164651
Couldn't classify 165675, 165721
Sorry, prediction pasa_asmbl_14686.p1 fails validation.
(GTG)	 GG	164514-164651	GT	CGG
(GGC)	 AG	165017-165104	GT	AGG
(GTG)	 AG	165221-165430	GT	TGG
(GCA)	 AG	165675-165721	AA	TGA
-recovered pasa_asmbl_14686.p1, internal, 165017, 165104
-recovered pasa_asmbl_14686.p1, internal, 165221, 165430
Valid prediction for CodingQuarry_transcript_18215-T1
Valid prediction for Augustus_model.g24857.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9535, rend_intergenic: 9356  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35338, rend_intergenic: 23589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41352, rend_intergenic: 37082  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66611, rend_intergenic: 58296  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97518, rend_intergenic: 86600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99912, rend_intergenic: 97868  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127589, rend_intergenic: 124573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157892, rend_intergenic: 148925  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166709, rend_intergenic: 159480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173656, rend_intergenic: 173070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185237, rend_intergenic: 183381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188290, rend_intergenic: 185399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193145, rend_intergenic: 189781  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 195707
-exon list size: 503


building trellis

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60.6    
60.8    
61.0    
61.2    
61.4    
61.6    
61.8    
62.0    
62.2    
62.4    
62.6    
62.8    
63.0    
63.2    
63.4    
63.6    
63.8    
64.0    
64.2    
64.4    
64.6    
64.8    
65.0    
65.1    
65.3    
65.5    
65.7    
65.9    
66.1    
66.3    
66.5    
66.7    
66.9    
67.1    
67.3    
67.5    
67.7    
67.9    
68.1    
68.3    
68.5    
68.7    
68.9    
69.1    
69.3    
69.5    
69.7    
69.9    
70.1    
70.3    
70.5    
70.7    
70.9    
71.1    
71.3    
71.5    
71.7    
71.9    
72.1    
72.3    
72.5    
72.7    
72.9    
73.1    
73.3    
73.5    
73.7    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.6    
76.8    
77.0    
77.2    
77.4    
77.6    
77.8    
78.0    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.4    
79.6    
79.8    
80.0    
80.2    
80.4    
80.6    
80.8    
81.0    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.8    
85.0    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.0    
95.2    
95.4    
95.6    
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 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 9535, rend_intergenic: 9356  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35338, rend_intergenic: 23589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41352, rend_intergenic: 37082  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66611, rend_intergenic: 58296  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97518, rend_intergenic: 86600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99912, rend_intergenic: 97868  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127589, rend_intergenic: 124573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157892, rend_intergenic: 148925  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166709, rend_intergenic: 159480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173656, rend_intergenic: 173070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185237, rend_intergenic: 183381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188290, rend_intergenic: 185399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193145, rend_intergenic: 189781  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