-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_18/scaffold_18_2575395-2837966

-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 Augustus_model.g27936.t1
Valid prediction for GlimmerHMM_glimmerT_41948-T1
Valid prediction for GlimmerHMM_glimmerT_41950-T1
Valid prediction for snap_scaffold_18-snap.550-T1
Valid prediction for snap_scaffold_18-snap.536-T1
Valid prediction for snap_scaffold_18-snap.539-T1
Valid prediction for Augustus_model.g27925.t1
Valid prediction for Augustus_model.g27924.t1
Valid prediction for GlimmerHMM_glimmerT_41947-T1
Valid prediction for snap_scaffold_18-snap.561-T1
Valid prediction for GlimmerHMM_glimmerT_41955-T1
Valid prediction for snap_scaffold_18-snap.575-T1
Valid prediction for GlimmerHMM_glimmerT_41932-T1
Valid prediction for snap_scaffold_18-snap.551-T1
Valid prediction for GlimmerHMM_glimmerT_41954-T1
Valid prediction for Augustus_model.g27929.t1
Valid prediction for GlimmerHMM_glimmerT_41935-T1
Valid prediction for snap_scaffold_18-snap.544-T1
Valid prediction for snap_scaffold_18-snap.531-T1
Valid prediction for snap_scaffold_18-snap.576-T1
Valid prediction for snap_scaffold_18-snap.574-T1
Valid prediction for snap_scaffold_18-snap.535-T1
Valid prediction for snap_scaffold_18-snap.553-T1
Valid prediction for snap_scaffold_18-snap.537-T1
Valid prediction for Augustus_model.g27928.t1
Valid prediction for snap_scaffold_18-snap.568-T1
Valid prediction for GlimmerHMM_glimmerT_41936-T1
Valid prediction for Augustus_model.g27932.t1
Valid prediction for snap_scaffold_18-snap.543-T1
Valid prediction for Augustus_model.g27937.t1
Valid prediction for snap_scaffold_18-snap.558-T1
Valid prediction for GlimmerHMM_glimmerT_41934-T1
Valid prediction for snap_scaffold_18-snap.577-T1
Valid prediction for GlimmerHMM_glimmerT_41943-T1
Valid prediction for snap_scaffold_18-snap.534-T1
Valid prediction for snap_scaffold_18-snap.570-T1
Valid prediction for GlimmerHMM_glimmerT_41945-T1
Valid prediction for snap_scaffold_18-snap.560-T1
Valid prediction for snap_scaffold_18-snap.562-T1
Valid prediction for GlimmerHMM_glimmerT_41939-T1
Valid prediction for Augustus_model.g27927.t1
Valid prediction for snap_scaffold_18-snap.580-T1
Valid prediction for snap_scaffold_18-snap.540-T1
Valid prediction for HiQ_model.g27939.t1
Valid prediction for snap_scaffold_18-snap.548-T1
Couldn't classify 220161, 220460
Sorry, prediction pasa_asmbl_20420.p1 fails validation.
(GAT)	 GG	220161-220460	GT	AGG
Valid prediction for snap_scaffold_18-snap.532-T1
Valid prediction for GlimmerHMM_glimmerT_41953-T1
Valid prediction for snap_scaffold_18-snap.546-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_18-snap.554-T1
Valid prediction for snap_scaffold_18-snap.564-T1
Valid prediction for GlimmerHMM_glimmerT_41937-T1
Valid prediction for snap_scaffold_18-snap.571-T1
Valid prediction for HiQ_model.g27935.t1
Valid prediction for HiQ_model.g27934.t1
Valid prediction for GlimmerHMM_glimmerT_41946-T1
Valid prediction for snap_scaffold_18-snap.549-T1
Valid prediction for snap_scaffold_18-snap.547-T1
Valid prediction for Augustus_model.g27930.t1
Valid prediction for snap_scaffold_18-snap.556-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_18-snap.538-T1
Valid prediction for GlimmerHMM_glimmerT_41949-T1
Valid prediction for snap_scaffold_18-snap.573-T1
Valid prediction for snap_scaffold_18-snap.572-T1
Valid prediction for snap_scaffold_18-snap.581-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_18-snap.559-T1
Valid prediction for snap_scaffold_18-snap.555-T1
Valid prediction for snap_scaffold_18-snap.565-T1
Valid prediction for Augustus_model.g27926.t1
Valid prediction for HiQ_model.g27933.t1
Valid prediction for GlimmerHMM_glimmerT_41941-T1
Valid prediction for snap_scaffold_18-snap.566-T1
Valid prediction for pasa_asmbl_19736.p1
Valid prediction for Augustus_model.g27938.t1
Valid prediction for snap_scaffold_18-snap.563-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_23702-T1
Valid prediction for GlimmerHMM_glimmerT_41944-T1
Valid prediction for GlimmerHMM_glimmerT_41940-T1
Valid prediction for snap_scaffold_18-snap.533-T1
Couldn't classify 116895, 116978
Sorry, prediction pasa_asmbl_19733.p1 fails validation.
(ATG)	 AA	111959-112260	GT	TGG
(GTA)	 AG	113024-113168	GT	AGG
(GTG)	 AG	113330-113518	GT	AGG
(CCC)	 AG	114238-114372	GT	TGG
(GAG)	 AG	115781-115921	GT	AGG
(GGC)	 AG	116685-116765	GT	AGG
(GTG)	 AG	116895-116978	AT	CGA
-recovered pasa_asmbl_19733.p1, initial, 111959, 112260
-recovered pasa_asmbl_19733.p1, internal, 113024, 113168
-recovered pasa_asmbl_19733.p1, internal, 113330, 113518
-recovered pasa_asmbl_19733.p1, internal, 114238, 114372
-recovered pasa_asmbl_19733.p1, internal, 115781, 115921
-recovered pasa_asmbl_19733.p1, internal, 116685, 116765
Valid prediction for snap_scaffold_18-snap.567-T1
Valid prediction for Augustus_model.g27931.t1
Valid prediction for snap_scaffold_18-snap.557-T1
Valid prediction for snap_scaffold_18-snap.545-T1
Valid prediction for Augustus_model.g27923.t1
Valid prediction for snap_scaffold_18-snap.552-T1
Valid prediction for snap_scaffold_18-snap.579-T1
Valid prediction for GlimmerHMM_glimmerT_41942-T1
Valid prediction for snap_scaffold_18-snap.569-T1
Valid prediction for snap_scaffold_18-snap.542-T1
Valid prediction for GlimmerHMM_glimmerT_41952-T1
Couldn't classify 131360, 131456
Sorry, prediction pasa_asmbl_19732.p1 fails validation.
(GAG)	 CA	131360-131456	GT	TGG
(TCA)	 AG	131827-131890	GT	AGG
(ACT)	 AG	133351-133432	GT	CCG
(GGT)	 AG	133771-133893	GT	AGG
(TCT)	 AG	134005-134104	GT	GGG
(ATC)	 AG	134248-134423	GT	AGG
(ATC)	 AG	135093-135176	GG	GAG
-recovered pasa_asmbl_19732.p1, terminal, 135093, 135176
-recovered pasa_asmbl_19732.p1, internal, 131827, 131890
-recovered pasa_asmbl_19732.p1, internal, 133351, 133432
-recovered pasa_asmbl_19732.p1, internal, 133771, 133893
-recovered pasa_asmbl_19732.p1, internal, 134005, 134104
-recovered pasa_asmbl_19732.p1, internal, 134248, 134423
Valid prediction for pasa_asmbl_19740.p1
Valid prediction for CodingQuarry_transcript_23700-T1
Valid prediction for GlimmerHMM_glimmerT_41933-T1
Valid prediction for snap_scaffold_18-snap.578-T1
Valid prediction for GlimmerHMM_glimmerT_41938-T1
Valid prediction for snap_scaffold_18-snap.541-T1
Valid prediction for pasa_asmbl_19735.p2
Valid prediction for GlimmerHMM_glimmerT_41951-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16789, rend_intergenic: 15926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44911, rend_intergenic: 41281  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56373, rend_intergenic: 45196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65242, rend_intergenic: 63954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68851, rend_intergenic: 65668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86210, rend_intergenic: 82636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96009, rend_intergenic: 91652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126111, rend_intergenic: 97381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135503, rend_intergenic: 130217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149870, rend_intergenic: 142990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170630, rend_intergenic: 169149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195827, rend_intergenic: 191956  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 245665, rend_intergenic: 239188  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 261777, rend_intergenic: 249071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 262572
-exon list size: 408


building trellis

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34.9    
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35.9    
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36.3    
36.6    
36.8    
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37.3    
37.6    
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38.0    
38.3    
38.5    
38.8    
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39.3    
39.5    
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40.5    
40.7    
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42.9    
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43.9    
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45.6    
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46.1    
46.3    
46.6    
46.8    
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47.6    
47.8    
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48.3    
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48.8    
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60.2    
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89.3    
89.5    
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90.2    
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91.0    
91.2    
91.5    
91.7    
92.0    
92.2    
92.4    
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92.9    
93.2    
93.4    
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93.9    
94.1    
94.4    
94.6    
94.9    
95.1    
95.4    
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96.1    
96.3    
96.6    
96.8    
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97.3    
97.6    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 16789, rend_intergenic: 15926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44911, rend_intergenic: 41281  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56373, rend_intergenic: 45196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65242, rend_intergenic: 63954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68851, rend_intergenic: 65668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86210, rend_intergenic: 82636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96009, rend_intergenic: 91652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126111, rend_intergenic: 97381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135503, rend_intergenic: 130217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149870, rend_intergenic: 142990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170630, rend_intergenic: 169149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195827, rend_intergenic: 191956  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 245665, rend_intergenic: 239188  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 261777, rend_intergenic: 249071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 13722
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11316
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support