-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_16006510-16206433

-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_1-snap.2822-T1
Valid prediction for GeneMark_model.3081_t
Valid prediction for Augustus_model.g1585.t1
Valid prediction for Augustus_model.g1584.t1
Valid prediction for Augustus_model.g1582.t1
Valid prediction for snap_scaffold_1-snap.2826-T1
Valid prediction for GlimmerHMM_glimmerT_2163-T1
Valid prediction for snap_scaffold_1-snap.2839-T1
Valid prediction for GeneMark_model.3080_t
Valid prediction for Augustus_model.g1598.t1
Valid prediction for GeneMark_model.3054_t
Valid prediction for snap_scaffold_1-snap.2854-T1
Valid prediction for GeneMark_model.3061_t
Valid prediction for HiQ_model.g1593.t1
Valid prediction for GeneMark_model.3083_t
Valid prediction for snap_scaffold_1-snap.2823-T1
Valid prediction for GlimmerHMM_glimmerT_2162-T1
Valid prediction for GlimmerHMM_glimmerT_2174-T1
Valid prediction for CodingQuarry_transcript_2943-T1
Valid prediction for GlimmerHMM_glimmerT_2170-T1
Valid prediction for GeneMark_model.3072_t
Valid prediction for Augustus_model.g1583.t1
Valid prediction for GeneMark_model.3051_t
Valid prediction for Augustus_model.g1589.t1
Valid prediction for GlimmerHMM_glimmerT_2176-T1
Valid prediction for GlimmerHMM_glimmerT_2182-T1
Valid prediction for pasa_asmbl_2444.p1
Valid prediction for Augustus_model.g1586.t1
Valid prediction for Augustus_model.g1581.t1
Valid prediction for GeneMark_model.3064_t
Valid prediction for GeneMark_model.3048_t
Valid prediction for Augustus_model.g1596.t1
Valid prediction for GlimmerHMM_glimmerT_2173-T1
Valid prediction for Augustus_model.g1590.t1
Valid prediction for GeneMark_model.3046_t
Valid prediction for GeneMark_model.3041_t
Valid prediction for snap_scaffold_1-snap.2848-T1
Valid prediction for GeneMark_model.3056_t
Valid prediction for GeneMark_model.3076_t
Valid prediction for snap_scaffold_1-snap.2835-T1
Valid prediction for snap_scaffold_1-snap.2853-T1
Valid prediction for GlimmerHMM_glimmerT_2165-T1
Valid prediction for snap_scaffold_1-snap.2829-T1
Valid prediction for snap_scaffold_1-snap.2817-T1
Valid prediction for snap_scaffold_1-snap.2825-T1
Valid prediction for GeneMark_model.3074_t
Valid prediction for GlimmerHMM_glimmerT_2166-T1
Valid prediction for GlimmerHMM_glimmerT_2164-T1
Valid prediction for GeneMark_model.3038_t
Valid prediction for GlimmerHMM_glimmerT_2168-T1
Valid prediction for GlimmerHMM_glimmerT_2188-T1
Valid prediction for GeneMark_model.3057_t
Valid prediction for GlimmerHMM_glimmerT_2161-T1
Valid prediction for GeneMark_model.3078_t
Valid prediction for GeneMark_model.3034_t
Valid prediction for Augustus_model.g1588.t1
Valid prediction for GeneMark_model.3042_t
Valid prediction for GeneMark_model.3067_t
Valid prediction for GeneMark_model.3062_t
Valid prediction for Augustus_model.g1587.t1
Valid prediction for snap_scaffold_1-snap.2821-T1
Valid prediction for GeneMark_model.3050_t
Valid prediction for snap_scaffold_1-snap.2833-T1
Valid prediction for GeneMark_model.3085_t
Valid prediction for snap_scaffold_1-snap.2824-T1
Valid prediction for snap_scaffold_1-snap.2813-T1
Valid prediction for GeneMark_model.3070_t
Couldn't classify 73374, 73622
Couldn't classify 74768, 74920
Sorry, prediction pasa_asmbl_2793.p1 fails validation.
(GAG)	 CC	73374-73622	GT	GGG
(CAC)	 AG	74768-74920	GT	CCG
-recovered pasa_asmbl_2793.p1, internal, 74768, 74920
Valid prediction for GeneMark_model.3052_t
Valid prediction for HiQ_model.g1594.t1
Valid prediction for snap_scaffold_1-snap.2838-T1
Valid prediction for GeneMark_model.3037_t
Valid prediction for GlimmerHMM_glimmerT_2172-T1
Valid prediction for snap_scaffold_1-snap.2828-T1
Valid prediction for GlimmerHMM_glimmerT_2169-T1
Valid prediction for snap_scaffold_1-snap.2815-T1
Valid prediction for GeneMark_model.3045_t
Valid prediction for GlimmerHMM_glimmerT_2179-T1
Valid prediction for GlimmerHMM_glimmerT_2171-T1
Valid prediction for snap_scaffold_1-snap.2856-T1
Valid prediction for snap_scaffold_1-snap.2827-T1
Valid prediction for GeneMark_model.3044_t
Valid prediction for snap_scaffold_1-snap.2841-T1
Couldn't classify 30195, 30195
Couldn't classify 36743, 36765
Sorry, prediction pasa_asmbl_2441.p1 fails validation.
(AGT)	 CA	30195-30195	GT	AAG
(TGA)	 AG	31124-31246	GT	GCG
(TGA)	 AG	33981-34103	GT	AAG
(ACC)	 AG	34845-34967	GT	CAG
(CCT)	 AG	35376-35605	GT	AGG
(GTG)	 AG	35778-35961	GT	AGG
(GTA)	 AG	36081-36233	GT	AGG
(AGG)	 AG	36743-36765	GT	AGG
-recovered pasa_asmbl_2441.p1, internal, 31124, 31246
-recovered pasa_asmbl_2441.p1, internal, 33981, 34103
-recovered pasa_asmbl_2441.p1, internal, 34845, 34967
-recovered pasa_asmbl_2441.p1, internal, 35376, 35605
-recovered pasa_asmbl_2441.p1, internal, 35778, 35961
-recovered pasa_asmbl_2441.p1, internal, 36081, 36233
-recovered pasa_asmbl_2441.p1, internal, 36743, 36765
Valid prediction for GeneMark_model.3047_t
Valid prediction for GlimmerHMM_glimmerT_2167-T1
Valid prediction for snap_scaffold_1-snap.2819-T1
Valid prediction for snap_scaffold_1-snap.2850-T1
Valid prediction for GeneMark_model.3059_t
Valid prediction for GeneMark_model.3065_t
Valid prediction for snap_scaffold_1-snap.2846-T1
Valid prediction for snap_scaffold_1-snap.2836-T1
Valid prediction for snap_scaffold_1-snap.2844-T1
Valid prediction for Augustus_model.g1602.t1
Valid prediction for snap_scaffold_1-snap.2831-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.3068_t
Valid prediction for GeneMark_model.3036_t
Valid prediction for GlimmerHMM_glimmerT_2184-T1
Valid prediction for GlimmerHMM_glimmerT_2186-T1
Valid prediction for GeneMark_model.3043_t
Valid prediction for Augustus_model.g1591.t1
Valid prediction for GeneMark_model.3060_t
Valid prediction for GlimmerHMM_glimmerT_2177-T1
Valid prediction for snap_scaffold_1-snap.2842-T1
Valid prediction for GlimmerHMM_glimmerT_2183-T1
Valid prediction for GeneMark_model.3049_t
Valid prediction for GlimmerHMM_glimmerT_2189-T1
Valid prediction for GlimmerHMM_glimmerT_2178-T1
Valid prediction for snap_scaffold_1-snap.2855-T1
Valid prediction for GeneMark_model.3075_t
Valid prediction for GeneMark_model.3055_t
Valid prediction for GeneMark_model.3035_t
Valid prediction for snap_scaffold_1-snap.2858-T1
Valid prediction for HiQ_model.g1592.t1
Valid prediction for snap_scaffold_1-snap.2840-T1
Valid prediction for snap_scaffold_1-snap.2837-T1
Valid prediction for GeneMark_model.3079_t
Valid prediction for GeneMark_model.3071_t
Valid prediction for GeneMark_model.3058_t
Valid prediction for snap_scaffold_1-snap.2812-T1
Valid prediction for CodingQuarry_transcript_2942-T1
Valid prediction for Augustus_model.g1595.t1
Valid prediction for GeneMark_model.3053_t
Valid prediction for Augustus_model.g1580.t1
Valid prediction for GeneMark_model.3040_t
Valid prediction for GeneMark_model.3082_t
Valid prediction for GlimmerHMM_glimmerT_2187-T1
Valid prediction for snap_scaffold_1-snap.2814-T1
Valid prediction for Augustus_model.g1597.t1
Valid prediction for snap_scaffold_1-snap.2811-T1
Valid prediction for GlimmerHMM_glimmerT_2159-T1
Valid prediction for GeneMark_model.3084_t
Valid prediction for snap_scaffold_1-snap.2830-T1
Valid prediction for GeneMark_model.3066_t
Valid prediction for GlimmerHMM_glimmerT_2175-T1
Valid prediction for snap_scaffold_1-snap.2847-T1
Valid prediction for snap_scaffold_1-snap.2849-T1
Valid prediction for GlimmerHMM_glimmerT_2160-T1
Valid prediction for Augustus_model.g1600.t1
Valid prediction for GeneMark_model.3077_t
Valid prediction for GeneMark_model.3063_t
Valid prediction for GlimmerHMM_glimmerT_2180-T1
Valid prediction for snap_scaffold_1-snap.2845-T1
Valid prediction for GlimmerHMM_glimmerT_2181-T1
Valid prediction for snap_scaffold_1-snap.2820-T1
Valid prediction for Augustus_model.g1603.t1
Valid prediction for GlimmerHMM_glimmerT_2185-T1
Valid prediction for snap_scaffold_1-snap.2816-T1
Valid prediction for snap_scaffold_1-snap.2832-T1
Valid prediction for snap_scaffold_1-snap.2834-T1
Valid prediction for snap_scaffold_1-snap.2857-T1
Valid prediction for snap_scaffold_1-snap.2818-T1
Valid prediction for snap_scaffold_1-snap.2843-T1
Valid prediction for snap_scaffold_1-snap.2852-T1
Valid prediction for GeneMark_model.3073_t
Couldn't classify 115203, 115334
Sorry, prediction pasa_asmbl_975.p1 fails validation.
(CAG)	 CG	115203-115334	GT	CGG
(GAT)	 AG	115447-115657	GT	GAG
(GAC)	 AG	118213-118361	GT	TGG
(ATG)	 AG	120436-120594	CC	AAC
-recovered pasa_asmbl_975.p1, terminal, 120436, 120594
-recovered pasa_asmbl_975.p1, internal, 115447, 115657
-recovered pasa_asmbl_975.p1, internal, 118213, 118361
Valid prediction for snap_scaffold_1-snap.2851-T1
Valid prediction for GeneMark_model.3039_t
Valid prediction for Augustus_model.g1601.t1
Valid prediction for Augustus_model.g1599.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10916, rend_intergenic: 7299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27771, rend_intergenic: 25650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29108, rend_intergenic: 29107  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35743, rend_intergenic: 32303  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37651, rend_intergenic: 35802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73447, rend_intergenic: 72312  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88026, rend_intergenic: 80948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107515, rend_intergenic: 105878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120685, rend_intergenic: 107578  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130641, rend_intergenic: 128502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136803, rend_intergenic: 134790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138977, rend_intergenic: 138346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147952, rend_intergenic: 139072  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149640, rend_intergenic: 148038  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158189, rend_intergenic: 153270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168669, rend_intergenic: 158657  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174070, rend_intergenic: 171502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177683, rend_intergenic: 174527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183940, rend_intergenic: 178532  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185613, rend_intergenic: 184926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188814, rend_intergenic: 186111  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195172, rend_intergenic: 189358  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 199924
-exon list size: 751


building trellis

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75.4    
75.6    
75.7    
75.8    
76.0    
76.1    
76.2    
76.4    
76.5    
76.6    
76.8    
76.9    
77.0    
77.2    
77.3    
77.4    
77.6    
77.7    
77.8    
78.0    
78.1    
78.2    
78.4    
78.5    
78.6    
78.8    
78.9    
79.0    
79.2    
79.3    
79.4    
79.5    
79.7    
79.8    
79.9    
80.1    
80.2    
80.3    
80.5    
80.6    
80.7    
80.9    
81.0    
81.1    
81.3    
81.4    
81.5    
81.7    
81.8    
81.9    
82.1    
82.2    
82.3    
82.5    
82.6    
82.7    
82.9    
83.0    
83.1    
83.3    
83.4    
83.5    
83.7    
83.8    
83.9    
84.1    
84.2    
84.3    
84.5    
84.6    
84.7    
84.9    
85.0    
85.1    
85.3    
85.4    
85.5    
85.7    
85.8    
85.9    
86.1    
86.2    
86.3    
86.5    
86.6    
86.7    
86.9    
87.0    
87.1    
87.3    
87.4    
87.5    
87.6    
87.8    
87.9    
88.0    
88.2    
88.3    
88.4    
88.6    
88.7    
88.8    
89.0    
89.1    
89.2    
89.4    
89.5    
89.6    
89.8    
89.9    
90.0    
90.2    
90.3    
90.4    
90.6    
90.7    
90.8    
91.0    
91.1    
91.2    
91.4    
91.5    
91.6    
91.8    
91.9    
92.0    
92.2    
92.3    
92.4    
92.6    
92.7    
92.8    
93.0    
93.1    
93.2    
93.4    
93.5    
93.6    
93.8    
93.9    
94.0    
94.2    
94.3    
94.4    
94.6    
94.7    
94.8    
95.0    
95.1    
95.2    
95.4    
95.5    
95.6    
95.8    
95.9    
96.0    
96.1    
96.3    
96.4    
96.5    
96.7    
96.8    
96.9    
97.1    
97.2    
97.3    
97.5    
97.6    
97.7    
97.9    
98.0    
98.1    
98.3    
98.4    
98.5    
98.7    
98.8    
98.9    
99.1    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 45 predictions from path traversal
Error with prediction: snap lend_intergenic: 10916, rend_intergenic: 7299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27771, rend_intergenic: 25650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29108, rend_intergenic: 29107  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35743, rend_intergenic: 32303  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37651, rend_intergenic: 35802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73447, rend_intergenic: 72312  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88026, rend_intergenic: 80948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107515, rend_intergenic: 105878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120685, rend_intergenic: 107578  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130641, rend_intergenic: 128502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136803, rend_intergenic: 134790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138977, rend_intergenic: 138346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147952, rend_intergenic: 139072  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149640, rend_intergenic: 148038  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158189, rend_intergenic: 153270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168669, rend_intergenic: 158657  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174070, rend_intergenic: 171502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177683, rend_intergenic: 174527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183940, rend_intergenic: 178532  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185613, rend_intergenic: 184926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188814, rend_intergenic: 186111  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195172, rend_intergenic: 189358  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