-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_16204830-16400616

-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.2883-T1
Valid prediction for GeneMark_model.3132_t
Couldn't classify 2979, 3455
Sorry, prediction pasa_asmbl_2446.p1 fails validation.
(TCT)	 TG	2979-3455	AC	ACA
Valid prediction for Augustus_model.g1609.t1
Valid prediction for GeneMark_model.3111_t
Valid prediction for Augustus_model.g1608.t1
Valid prediction for snap_scaffold_1-snap.2859-T1
Valid prediction for GeneMark_model.3126_t
Valid prediction for GeneMark_model.3117_t
Valid prediction for GeneMark_model.3116_t
Valid prediction for CodingQuarry_transcript_2945-T1
Valid prediction for snap_scaffold_1-snap.2899-T1
Valid prediction for snap_scaffold_1-snap.2865-T1
Valid prediction for snap_scaffold_1-snap.2891-T1
Valid prediction for GlimmerHMM_glimmerT_2204-T1
Valid prediction for GlimmerHMM_glimmerT_2198-T1
Valid prediction for snap_scaffold_1-snap.2870-T1
Valid prediction for snap_scaffold_1-snap.2868-T1
Valid prediction for snap_scaffold_1-snap.2873-T1
Valid prediction for GlimmerHMM_glimmerT_2192-T1
Couldn't classify 118604, 118615
Couldn't classify 120443, 120563
Sorry, prediction pasa_asmbl_2457.p1 fails validation.
(CCT)	 AA	118604-118615	GT	AGG
(AAT)	 AG	118778-118963	GT	AGG
(TGG)	 AG	119282-119443	GT	AGG
(CTT)	 AG	120240-120340	GT	GAG
(GCA)	 AG	120443-120563	GT	TGG
-recovered pasa_asmbl_2457.p1, internal, 118778, 118963
-recovered pasa_asmbl_2457.p1, internal, 119282, 119443
-recovered pasa_asmbl_2457.p1, internal, 120240, 120340
-recovered pasa_asmbl_2457.p1, internal, 120443, 120563
Valid prediction for snap_scaffold_1-snap.2863-T1
Valid prediction for GeneMark_model.3106_t
Valid prediction for GeneMark_model.3092_t
Valid prediction for GlimmerHMM_glimmerT_2214-T1
Valid prediction for GeneMark_model.3135_t
Valid prediction for snap_scaffold_1-snap.2897-T1
Valid prediction for GlimmerHMM_glimmerT_2196-T1
Valid prediction for GeneMark_model.3114_t
Valid prediction for GeneMark_model.3122_t
Valid prediction for GeneMark_model.3104_t
Valid prediction for snap_scaffold_1-snap.2886-T1
Valid prediction for Augustus_model.g1607.t1
Valid prediction for snap_scaffold_1-snap.2877-T1
Valid prediction for snap_scaffold_1-snap.2875-T1
Valid prediction for GlimmerHMM_glimmerT_2199-T1
Valid prediction for GeneMark_model.3099_t
Valid prediction for GeneMark_model.3131_t
Valid prediction for GlimmerHMM_glimmerT_2207-T1
Valid prediction for snap_scaffold_1-snap.2880-T1
Valid prediction for snap_scaffold_1-snap.2864-T1
Valid prediction for GlimmerHMM_glimmerT_2200-T1
Valid prediction for CodingQuarry_transcript_2946-T1
Valid prediction for pasa_asmbl_2448.p1
Valid prediction for snap_scaffold_1-snap.2895-T1
Valid prediction for GeneMark_model.3094_t
Valid prediction for GeneMark_model.3109_t
Valid prediction for GeneMark_model.3102_t
Valid prediction for Augustus_model.g1611.t1
Valid prediction for GeneMark_model.3124_t
Valid prediction for Augustus_model.g1617.t1
Valid prediction for snap_scaffold_1-snap.2890-T1
Valid prediction for GeneMark_model.3128_t
Valid prediction for Augustus_model.g1606.t1
Valid prediction for GeneMark_model.3133_t
Couldn't classify 117784, 117940
Couldn't classify 118060, 118397
Sorry, prediction pasa_asmbl_2456.p1 fails validation.
(GGG)	 AG	117784-117940	GT	GGG
(CTC)	 AG	118060-118397	CA	ACC
-recovered pasa_asmbl_2456.p1, internal, 117784, 117940
Valid prediction for GeneMark_model.3088_t
Valid prediction for Augustus_model.g1604.t1
Valid prediction for GeneMark_model.3096_t
Valid prediction for GlimmerHMM_glimmerT_2194-T1
Valid prediction for GlimmerHMM_glimmerT_2190-T1
Valid prediction for GeneMark_model.3090_t
Valid prediction for GlimmerHMM_glimmerT_2193-T1
Valid prediction for snap_scaffold_1-snap.2869-T1
Valid prediction for snap_scaffold_1-snap.2862-T1
Valid prediction for snap_scaffold_1-snap.2889-T1
Valid prediction for GlimmerHMM_glimmerT_2205-T1
Valid prediction for snap_scaffold_1-snap.2882-T1
Valid prediction for CodingQuarry_transcript_2944-T1
Valid prediction for GeneMark_model.3107_t
Valid prediction for HiQ_model.g1605.t1
Valid prediction for GlimmerHMM_glimmerT_2209-T1
Valid prediction for Augustus_model.g1615.t1
Valid prediction for GlimmerHMM_glimmerT_2195-T1
Valid prediction for GeneMark_model.3086_t
Valid prediction for Augustus_model.g1623.t1
Valid prediction for GlimmerHMM_glimmerT_2217-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_1-snap.2867-T1
Valid prediction for GlimmerHMM_glimmerT_2191-T1
Valid prediction for snap_scaffold_1-snap.2902-T1
Valid prediction for GeneMark_model.3087_t
Valid prediction for GeneMark_model.3112_t
Valid prediction for pasa_asmbl_986.p1
Valid prediction for GeneMark_model.3089_t
Valid prediction for GlimmerHMM_glimmerT_2197-T1
Valid prediction for Augustus_model.g1613.t1
Valid prediction for snap_scaffold_1-snap.2871-T1
Valid prediction for snap_scaffold_1-snap.2876-T1
Valid prediction for GlimmerHMM_glimmerT_2208-T1
Valid prediction for Augustus_model.g1612.t1
Valid prediction for GlimmerHMM_glimmerT_2202-T1
Valid prediction for snap_scaffold_1-snap.2892-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.2887-T1
Valid prediction for GlimmerHMM_glimmerT_2215-T1
Valid prediction for HiQ_model.g1619.t1
Valid prediction for snap_scaffold_1-snap.2874-T1
Valid prediction for snap_scaffold_1-snap.2884-T1
Valid prediction for snap_scaffold_1-snap.2861-T1
Valid prediction for snap_scaffold_1-snap.2860-T1
Valid prediction for GlimmerHMM_glimmerT_2216-T1
Valid prediction for GeneMark_model.3137_t
Valid prediction for GlimmerHMM_glimmerT_2218-T1
Valid prediction for GeneMark_model.3120_t
Valid prediction for GeneMark_model.3118_t
Valid prediction for GeneMark_model.3101_t
Valid prediction for snap_scaffold_1-snap.2900-T1
Valid prediction for Augustus_model.g1622.t1
Valid prediction for GeneMark_model.3121_t
Valid prediction for GeneMark_model.3097_t
Valid prediction for Augustus_model.g1624.t1
Couldn't classify 44640, 44794
Couldn't classify 45597, 45710
Sorry, prediction pasa_asmbl_1329.p1 fails validation.
(CCA)	 CC	44640-44794	GT	CAG
(CAC)	 AG	45182-45224	GT	GGG
(ATC)	 AG	45597-45710	CC	GAC
-recovered pasa_asmbl_1329.p1, internal, 45182, 45224
Valid prediction for GeneMark_model.3100_t
Valid prediction for GeneMark_model.3095_t
Valid prediction for GeneMark_model.3129_t
Valid prediction for GeneMark_model.3130_t
Valid prediction for snap_scaffold_1-snap.2903-T1
Valid prediction for snap_scaffold_1-snap.2885-T1
Valid prediction for GlimmerHMM_glimmerT_2219-T1
Valid prediction for GeneMark_model.3123_t
Valid prediction for Augustus_model.g1621.t1
Valid prediction for Augustus_model.g1620.t1
Valid prediction for Augustus_model.g1614.t1
Valid prediction for snap_scaffold_1-snap.2878-T1
Valid prediction for snap_scaffold_1-snap.2901-T1
Couldn't classify 46265, 46366
Sorry, prediction pasa_asmbl_989.p1 fails validation.
(TAT)	 AG	46265-46366	GT	AGG
(TGG)	 AG	46504-46605	GT	AGG
(CCC)	 AG	46872-47033	GT	AGG
(ATC)	 AG	47224-47321	GT	AGG
(CGT)	 AG	47514-47649	GT	AGG
(ATC)	 AG	48312-48434	GT	AGG
(ACC)	 AG	50166-50267	GT	AGG
(GTC)	 AG	50966-51019	GG	GAG
-recovered pasa_asmbl_989.p1, terminal, 50966, 51019
-recovered pasa_asmbl_989.p1, internal, 46265, 46366
-recovered pasa_asmbl_989.p1, internal, 46504, 46605
-recovered pasa_asmbl_989.p1, internal, 46872, 47033
-recovered pasa_asmbl_989.p1, internal, 47224, 47321
-recovered pasa_asmbl_989.p1, internal, 47514, 47649
-recovered pasa_asmbl_989.p1, internal, 48312, 48434
-recovered pasa_asmbl_989.p1, internal, 50166, 50267
Valid prediction for GeneMark_model.3098_t
Valid prediction for GlimmerHMM_glimmerT_2203-T1
Valid prediction for GlimmerHMM_glimmerT_2212-T1
Valid prediction for GlimmerHMM_glimmerT_2210-T1
Valid prediction for GeneMark_model.3136_t
Valid prediction for GeneMark_model.3127_t
Valid prediction for Augustus_model.g1618.t1
Valid prediction for snap_scaffold_1-snap.2898-T1
Valid prediction for snap_scaffold_1-snap.2879-T1
Valid prediction for GeneMark_model.3093_t
Couldn't classify 103961, 104065
Sorry, prediction pasa_asmbl_980.p2 fails validation.
(GTC)	 CA	103961-104065	GT	TGG
(TGG)	 AG	105684-105764	GT	CGG
(CAC)	 AG	106180-106359	GT	GGG
(GAA)	 AG	107624-107788	AG	AGA
-recovered pasa_asmbl_980.p2, terminal, 107624, 107788
-recovered pasa_asmbl_980.p2, internal, 105684, 105764
-recovered pasa_asmbl_980.p2, internal, 106180, 106359
Valid prediction for GlimmerHMM_glimmerT_2220-T1
Valid prediction for GeneMark_model.3125_t
Valid prediction for snap_scaffold_1-snap.2894-T1
Valid prediction for snap_scaffold_1-snap.2866-T1
Valid prediction for GeneMark_model.3113_t
Valid prediction for GeneMark_model.3134_t
Valid prediction for GeneMark_model.3091_t
Valid prediction for GlimmerHMM_glimmerT_2211-T1
Valid prediction for GeneMark_model.3105_t
Valid prediction for GeneMark_model.3110_t
Valid prediction for Augustus_model.g1610.t1
Couldn't classify 28975, 29087
Sorry, prediction pasa_asmbl_991.p1 fails validation.
(ACT)	 AG	28975-29087	GT	GCG
(GGA)	 AG	30941-31032	GT	GGG
(GTG)	 AG	31400-31479	GT	AGG
(GTG)	 AG	33366-33464	GT	ACG
(GCT)	 AG	34760-34855	AT	GAA
-recovered pasa_asmbl_991.p1, terminal, 34760, 34855
-recovered pasa_asmbl_991.p1, internal, 28975, 29087
-recovered pasa_asmbl_991.p1, internal, 30941, 31032
-recovered pasa_asmbl_991.p1, internal, 31400, 31479
-recovered pasa_asmbl_991.p1, internal, 33366, 33464
Valid prediction for snap_scaffold_1-snap.2881-T1
Valid prediction for GlimmerHMM_glimmerT_2213-T1
Valid prediction for GeneMark_model.3108_t
Valid prediction for GeneMark_model.3103_t
Valid prediction for pasa_asmbl_988.p1
Valid prediction for GlimmerHMM_glimmerT_2201-T1
Valid prediction for snap_scaffold_1-snap.2872-T1
Valid prediction for GeneMark_model.3115_t
Valid prediction for HiQ_model.g1616.t1
Valid prediction for GlimmerHMM_glimmerT_2206-T1
Valid prediction for snap_scaffold_1-snap.2896-T1
Valid prediction for snap_scaffold_1-snap.2888-T1
Valid prediction for snap_scaffold_1-snap.2893-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 42601, rend_intergenic: 39306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57745, rend_intergenic: 49770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67322, rend_intergenic: 62056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73372, rend_intergenic: 68061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82815, rend_intergenic: 81546  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90781, rend_intergenic: 88049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96950, rend_intergenic: 92325  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122433, rend_intergenic: 114958  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132608, rend_intergenic: 128678  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163012, rend_intergenic: 161212  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171437, rend_intergenic: 166704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 195787
-exon list size: 724


building trellis

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77.0    
77.1    
77.3    
77.4    
77.5    
77.7    
77.8    
78.0    
78.1    
78.2    
78.4    
78.5    
78.7    
78.8    
78.9    
79.1    
79.2    
79.3    
79.5    
79.6    
79.8    
79.9    
80.0    
80.2    
80.3    
80.4    
80.6    
80.7    
80.9    
81.0    
81.1    
81.3    
81.4    
81.5    
81.7    
81.8    
82.0    
82.1    
82.2    
82.4    
82.5    
82.6    
82.8    
82.9    
83.1    
83.2    
83.3    
83.5    
83.6    
83.7    
83.9    
84.0    
84.2    
84.3    
84.4    
84.6    
84.7    
84.8    
85.0    
85.1    
85.3    
85.4    
85.5    
85.7    
85.8    
86.0    
86.1    
86.2    
86.4    
86.5    
86.6    
86.8    
86.9    
87.1    
87.2    
87.3    
87.5    
87.6    
87.7    
87.9    
88.0    
88.2    
88.3    
88.4    
88.6    
88.7    
88.8    
89.0    
89.1    
89.3    
89.4    
89.5    
89.7    
89.8    
89.9    
90.1    
90.2    
90.4    
90.5    
90.6    
90.8    
90.9    
91.0    
91.2    
91.3    
91.5    
91.6    
91.7    
91.9    
92.0    
92.1    
92.3    
92.4    
92.6    
92.7    
92.8    
93.0    
93.1    
93.3    
93.4    
93.5    
93.7    
93.8    
93.9    
94.1    
94.2    
94.4    
94.5    
94.6    
94.8    
94.9    
95.0    
95.2    
95.3    
95.5    
95.6    
95.7    
95.9    
96.0    
96.1    
96.3    
96.4    
96.6    
96.7    
96.8    
97.0    
97.1    
97.2    
97.4    
97.5    
97.7    
97.8    
97.9    
98.1    
98.2    
98.3    
98.5    
98.6    
98.8    
98.9    
99.0    
99.2    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 42601, rend_intergenic: 39306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57745, rend_intergenic: 49770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67322, rend_intergenic: 62056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73372, rend_intergenic: 68061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82815, rend_intergenic: 81546  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90781, rend_intergenic: 88049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96950, rend_intergenic: 92325  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122433, rend_intergenic: 114958  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132608, rend_intergenic: 128678  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163012, rend_intergenic: 161212  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171437, rend_intergenic: 166704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support