-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_14651717-14858007

-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.g21898.t1
Valid prediction for GlimmerHMM_glimmerT_32832-T1
Valid prediction for GlimmerHMM_glimmerT_32819-T1
Valid prediction for GlimmerHMM_glimmerT_32831-T1
Valid prediction for snap_scaffold_13-snap.2856-T1
Valid prediction for GlimmerHMM_glimmerT_32812-T1
Valid prediction for Augustus_model.g21899.t1
Valid prediction for snap_scaffold_13-snap.2842-T1
Valid prediction for Augustus_model.g21891.t1
Couldn't classify 52135, 52230
Couldn't classify 53513, 53606
Sorry, prediction pasa_asmbl_11465.p1 fails validation.
(GTG)	 AG	52135-52230	GT	AGG
(GTG)	 AG	52482-52663	GT	TGG
(GTG)	 AG	53513-53606	CA	GAC
-recovered pasa_asmbl_11465.p1, internal, 52135, 52230
-recovered pasa_asmbl_11465.p1, internal, 52482, 52663
Valid prediction for snap_scaffold_13-snap.2850-T1
Valid prediction for GlimmerHMM_glimmerT_32820-T1
Valid prediction for snap_scaffold_13-snap.2831-T1
Valid prediction for snap_scaffold_13-snap.2857-T1
Valid prediction for GlimmerHMM_glimmerT_32827-T1
Valid prediction for snap_scaffold_13-snap.2836-T1
Valid prediction for snap_scaffold_13-snap.2818-T1
Valid prediction for Augustus_model.g21894.t1
Valid prediction for GlimmerHMM_glimmerT_32818-T1
Valid prediction for snap_scaffold_13-snap.2819-T1
Valid prediction for snap_scaffold_13-snap.2847-T1
Valid prediction for snap_scaffold_13-snap.2822-T1
Valid prediction for GlimmerHMM_glimmerT_32815-T1
Valid prediction for snap_scaffold_13-snap.2854-T1
Valid prediction for snap_scaffold_13-snap.2852-T1
Valid prediction for snap_scaffold_13-snap.2814-T1
Valid prediction for snap_scaffold_13-snap.2821-T1
Valid prediction for snap_scaffold_13-snap.2824-T1
Valid prediction for pasa_asmbl_11660.p1
Valid prediction for snap_scaffold_13-snap.2853-T1
Valid prediction for snap_scaffold_13-snap.2810-T1
Couldn't classify 27287, 27350
Sorry, prediction pasa_asmbl_11626.p1 fails validation.
(ATG)	 TG	24752-24761	GT	GGG
(ACG)	 AG	24935-25020	GT	AGG
(GGT)	 AG	25109-25172	GT	TGG
(GTG)	 AG	26303-26370	GT	AGG
(GTG)	 AG	26893-26963	GT	GTG
(GCT)	 AG	27287-27350	AT	CCA
-recovered pasa_asmbl_11626.p1, initial, 24752, 24761
-recovered pasa_asmbl_11626.p1, internal, 24935, 25020
-recovered pasa_asmbl_11626.p1, internal, 25109, 25172
-recovered pasa_asmbl_11626.p1, internal, 26303, 26370
-recovered pasa_asmbl_11626.p1, internal, 26893, 26963
Valid prediction for Augustus_model.g21897.t1
Valid prediction for Augustus_model.g21896.t1
Valid prediction for snap_scaffold_13-snap.2840-T1
Valid prediction for snap_scaffold_13-snap.2832-T1
Valid prediction for snap_scaffold_13-snap.2825-T1
Valid prediction for CodingQuarry_transcript_13316-T1
Valid prediction for snap_scaffold_13-snap.2830-T1
Couldn't classify 59060, 59149
Couldn't classify 59571, 59879
Sorry, prediction pasa_asmbl_11466.p1 fails validation.
(CAC)	 TC	59060-59149	GT	AAG
(GTT)	 AG	59571-59879	CC	CCC
Valid prediction for Augustus_model.g21895.t1
Valid prediction for snap_scaffold_13-snap.2860-T1
Valid prediction for Augustus_model.g21892.t1
Valid prediction for GlimmerHMM_glimmerT_32828-T1
Valid prediction for snap_scaffold_13-snap.2848-T1
Valid prediction for snap_scaffold_13-snap.2859-T1
Valid prediction for snap_scaffold_13-snap.2846-T1
Valid prediction for snap_scaffold_13-snap.2827-T1
Valid prediction for GlimmerHMM_glimmerT_32816-T1
Valid prediction for GlimmerHMM_glimmerT_32834-T1
Valid prediction for GlimmerHMM_glimmerT_32824-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.2820-T1
Valid prediction for GlimmerHMM_glimmerT_32817-T1
Valid prediction for GlimmerHMM_glimmerT_32830-T1
Valid prediction for snap_scaffold_13-snap.2833-T1
Valid prediction for GlimmerHMM_glimmerT_32829-T1
Valid prediction for snap_scaffold_13-snap.2823-T1
Valid prediction for snap_scaffold_13-snap.2844-T1
Valid prediction for snap_scaffold_13-snap.2835-T1
Valid prediction for snap_scaffold_13-snap.2849-T1
Valid prediction for GlimmerHMM_glimmerT_32826-T1
Valid prediction for snap_scaffold_13-snap.2838-T1
Valid prediction for snap_scaffold_13-snap.2858-T1
Valid prediction for snap_scaffold_13-snap.2812-T1
Valid prediction for GlimmerHMM_glimmerT_32837-T1
Valid prediction for snap_scaffold_13-snap.2813-T1
Valid prediction for GlimmerHMM_glimmerT_32814-T1
Valid prediction for snap_scaffold_13-snap.2829-T1
Valid prediction for snap_scaffold_13-snap.2828-T1
Valid prediction for snap_scaffold_13-snap.2855-T1
Valid prediction for snap_scaffold_13-snap.2851-T1
Valid prediction for GlimmerHMM_glimmerT_32822-T1
Valid prediction for GlimmerHMM_glimmerT_32825-T1
Valid prediction for GlimmerHMM_glimmerT_32823-T1
Valid prediction for snap_scaffold_13-snap.2816-T1
Valid prediction for snap_scaffold_13-snap.2841-T1
Valid prediction for GlimmerHMM_glimmerT_32821-T1
Valid prediction for Augustus_model.g21893.t1
Valid prediction for snap_scaffold_13-snap.2817-T1
Valid prediction for snap_scaffold_13-snap.2834-T1
Valid prediction for GlimmerHMM_glimmerT_32836-T1
Valid prediction for snap_scaffold_13-snap.2839-T1
Valid prediction for GlimmerHMM_glimmerT_32833-T1
Valid prediction for GlimmerHMM_glimmerT_32835-T1
Valid prediction for snap_scaffold_13-snap.2843-T1
Valid prediction for Augustus_model.g21901.t1
Valid prediction for snap_scaffold_13-snap.2845-T1
Valid prediction for snap_scaffold_13-snap.2826-T1
Valid prediction for snap_scaffold_13-snap.2811-T1
Valid prediction for Augustus_model.g21900.t1
Valid prediction for GlimmerHMM_glimmerT_32813-T1
Couldn't classify 30418, 30521
Couldn't classify 33556, 33596
Sorry, prediction pasa_asmbl_10207.p1 fails validation.
(GCA)	 CA	30418-30521	GT	AGG
(AGA)	 AG	30892-30989	GT	AAG
(AAA)	 AG	32018-32287	GT	AGG
(TTC)	 AG	33556-33596	GA	TGG
-recovered pasa_asmbl_10207.p1, internal, 30892, 30989
-recovered pasa_asmbl_10207.p1, internal, 32018, 32287
Valid prediction for snap_scaffold_13-snap.2815-T1
Valid prediction for snap_scaffold_13-snap.2837-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9894, rend_intergenic: 6100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26658, rend_intergenic: 16527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28518, rend_intergenic: 26667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43818, rend_intergenic: 42484  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59834, rend_intergenic: 43886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70826, rend_intergenic: 64762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75374, rend_intergenic: 71282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85181, rend_intergenic: 77009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86201, rend_intergenic: 85560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88812, rend_intergenic: 86271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95508, rend_intergenic: 88901  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102632, rend_intergenic: 98121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106418, rend_intergenic: 103024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115255, rend_intergenic: 106914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119639, rend_intergenic: 116444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121231, rend_intergenic: 120474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123627, rend_intergenic: 121234  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125866, rend_intergenic: 123778  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157148, rend_intergenic: 138766  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165233, rend_intergenic: 161182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178867, rend_intergenic: 168219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197842, rend_intergenic: 185935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201691, rend_intergenic: 198324  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203993, rend_intergenic: 201879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 206291
-exon list size: 357


building trellis

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28.4    
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30.6    
30.9    
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33.4    
33.7    
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34.8    
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36.2    
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40.9    
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47.4    
47.6    
47.9    
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50.4    
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51.5    
51.8    
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52.4    
52.6    
52.9    
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54.3    
54.6    
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55.2    
55.4    
55.7    
56.0    
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78.6    
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79.4    
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84.4    
84.7    
85.0    
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86.6    
86.9    
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88.3    
88.6    
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89.1    
89.4    
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90.0    
90.3    
90.5    
90.8    
91.1    
91.4    
91.6    
91.9    
92.2    
92.5    
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93.0    
93.3    
93.6    
93.9    
94.2    
94.4    
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95.5    
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96.1    
96.4    
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97.2    
97.5    
97.8    
98.1    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 9894, rend_intergenic: 6100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26658, rend_intergenic: 16527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28518, rend_intergenic: 26667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43818, rend_intergenic: 42484  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59834, rend_intergenic: 43886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70826, rend_intergenic: 64762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75374, rend_intergenic: 71282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85181, rend_intergenic: 77009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86201, rend_intergenic: 85560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88812, rend_intergenic: 86271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95508, rend_intergenic: 88901  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102632, rend_intergenic: 98121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106418, rend_intergenic: 103024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115255, rend_intergenic: 106914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119639, rend_intergenic: 116444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121231, rend_intergenic: 120474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123627, rend_intergenic: 121234  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125866, rend_intergenic: 123778  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157148, rend_intergenic: 138766  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165233, rend_intergenic: 161182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178867, rend_intergenic: 168219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197842, rend_intergenic: 185935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201691, rend_intergenic: 198324  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203993, rend_intergenic: 201879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support