-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_14997851-15197070

-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 HiQ_model.g15595.t1
Valid prediction for snap_scaffold_9-snap.3041-T1
Valid prediction for snap_scaffold_9-snap.3060-T1
Valid prediction for snap_scaffold_9-snap.3062-T1
Valid prediction for GlimmerHMM_glimmerT_23412-T1
Valid prediction for snap_scaffold_9-snap.3070-T1
Valid prediction for CodingQuarry_transcript_62411-T1
Valid prediction for GlimmerHMM_glimmerT_23419-T1
Valid prediction for GlimmerHMM_glimmerT_23417-T1
Couldn't classify 88181, 88262
Sorry, prediction pasa_asmbl_54546.p1 fails validation.
(GGG)	 GA	88181-88262	GT	AGG
(GTC)	 AG	88358-88459	GT	AGG
(CCA)	 AG	88988-89140	GT	CGG
(GCG)	 AG	89445-89539	GT	TGG
(GTG)	 AG	89640-89699	CG	AGC
-recovered pasa_asmbl_54546.p1, terminal, 89640, 89699
-recovered pasa_asmbl_54546.p1, internal, 88358, 88459
-recovered pasa_asmbl_54546.p1, internal, 88988, 89140
-recovered pasa_asmbl_54546.p1, internal, 89445, 89539
Valid prediction for snap_scaffold_9-snap.3080-T1
Valid prediction for snap_scaffold_9-snap.3053-T1
Valid prediction for CodingQuarry_transcript_62410-T1
Valid prediction for Augustus_model.g15603.t1
Valid prediction for snap_scaffold_9-snap.3068-T1
Valid prediction for GlimmerHMM_glimmerT_23427-T1
Valid prediction for GlimmerHMM_glimmerT_23422-T1
Couldn't classify 75864, 76057
Sorry, prediction pasa_asmbl_54545.p1 fails validation.
(CCA)	 TT	75864-76057	GT	CGG
(CTC)	 AG	76797-77265	GT	GGG
(GAC)	 AG	77353-77531	GT	AGG
(TGA)	 AG	77621-77795	AG	AAA
-recovered pasa_asmbl_54545.p1, terminal, 77621, 77795
-recovered pasa_asmbl_54545.p1, internal, 76797, 77265
-recovered pasa_asmbl_54545.p1, internal, 77353, 77531
Valid prediction for snap_scaffold_9-snap.3077-T1
Valid prediction for snap_scaffold_9-snap.3074-T1
Valid prediction for GlimmerHMM_glimmerT_23423-T1
Valid prediction for snap_scaffold_9-snap.3046-T1
Valid prediction for snap_scaffold_9-snap.3038-T1
Valid prediction for snap_scaffold_9-snap.3050-T1
Valid prediction for Augustus_model.g15590.t1
Valid prediction for GlimmerHMM_glimmerT_23418-T1
Valid prediction for snap_scaffold_9-snap.3036-T1
Valid prediction for GlimmerHMM_glimmerT_23440-T1
Valid prediction for Augustus_model.g15597.t1
Valid prediction for Augustus_model.g15594.t1
Valid prediction for Augustus_model.g15600.t1
Valid prediction for snap_scaffold_9-snap.3064-T1
Valid prediction for snap_scaffold_9-snap.3066-T1
Valid prediction for snap_scaffold_9-snap.3073-T1
Valid prediction for snap_scaffold_9-snap.3039-T1
Valid prediction for snap_scaffold_9-snap.3051-T1
Valid prediction for Augustus_model.g15589.t1
Valid prediction for snap_scaffold_9-snap.3047-T1
Valid prediction for snap_scaffold_9-snap.3057-T1
Valid prediction for snap_scaffold_9-snap.3056-T1
Valid prediction for GlimmerHMM_glimmerT_23431-T1
Valid prediction for GlimmerHMM_glimmerT_23432-T1
Valid prediction for snap_scaffold_9-snap.3035-T1
Valid prediction for snap_scaffold_9-snap.3037-T1
Valid prediction for snap_scaffold_9-snap.3071-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_23437-T1
Valid prediction for GlimmerHMM_glimmerT_23415-T1
Valid prediction for GlimmerHMM_glimmerT_23433-T1
Valid prediction for snap_scaffold_9-snap.3072-T1
Valid prediction for GlimmerHMM_glimmerT_23436-T1
Valid prediction for snap_scaffold_9-snap.3049-T1
Valid prediction for snap_scaffold_9-snap.3079-T1
Valid prediction for snap_scaffold_9-snap.3075-T1
Valid prediction for snap_scaffold_9-snap.3058-T1
Valid prediction for snap_scaffold_9-snap.3042-T1
Valid prediction for Augustus_model.g15609.t1
Valid prediction for GlimmerHMM_glimmerT_23411-T1
Valid prediction for GlimmerHMM_glimmerT_23409-T1
Valid prediction for snap_scaffold_9-snap.3044-T1
Valid prediction for snap_scaffold_9-snap.3076-T1
Valid prediction for GlimmerHMM_glimmerT_23416-T1
Valid prediction for Augustus_model.g15596.t1
Valid prediction for snap_scaffold_9-snap.3069-T1
Valid prediction for GlimmerHMM_glimmerT_23439-T1
Valid prediction for GlimmerHMM_glimmerT_23410-T1
Valid prediction for GlimmerHMM_glimmerT_23426-T1
Valid prediction for GlimmerHMM_glimmerT_23413-T1
Valid prediction for GlimmerHMM_glimmerT_23425-T1
Valid prediction for GlimmerHMM_glimmerT_23414-T1
Valid prediction for Augustus_model.g15592.t1
Valid prediction for snap_scaffold_9-snap.3078-T1
Valid prediction for GlimmerHMM_glimmerT_23441-T1
Valid prediction for Augustus_model.g15612.t1
Valid prediction for snap_scaffold_9-snap.3059-T1
Valid prediction for Augustus_model.g15608.t1
Valid prediction for GlimmerHMM_glimmerT_23435-T1
Valid prediction for snap_scaffold_9-snap.3055-T1
Valid prediction for GlimmerHMM_glimmerT_23421-T1
Valid prediction for snap_scaffold_9-snap.3065-T1
Valid prediction for Augustus_model.g15613.t1
Valid prediction for snap_scaffold_9-snap.3043-T1
Valid prediction for Augustus_model.g15591.t1
Valid prediction for snap_scaffold_9-snap.3052-T1
Valid prediction for snap_scaffold_9-snap.3061-T1
Valid prediction for Augustus_model.g15593.t1
Valid prediction for snap_scaffold_9-snap.3063-T1
Valid prediction for Augustus_model.g15598.t1
Valid prediction for GlimmerHMM_glimmerT_23438-T1
Valid prediction for Augustus_model.g15607.t1
Valid prediction for Augustus_model.g15599.t1
Valid prediction for GlimmerHMM_glimmerT_23429-T1
Couldn't classify 34174, 34710
Sorry, prediction pasa_asmbl_55509.p1 fails validation.
(GTA)	 CT	34174-34710	GC	GAG
Valid prediction for Augustus_model.g15602.t1
Valid prediction for snap_scaffold_9-snap.3045-T1
Valid prediction for snap_scaffold_9-snap.3054-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g15601.t1
Valid prediction for snap_scaffold_9-snap.3067-T1
Valid prediction for Augustus_model.g15604.t1
Valid prediction for GlimmerHMM_glimmerT_23428-T1
Valid prediction for GlimmerHMM_glimmerT_23434-T1
Valid prediction for Augustus_model.g15611.t1
Valid prediction for snap_scaffold_9-snap.3040-T1
Valid prediction for Augustus_model.g15606.t1
Valid prediction for snap_scaffold_9-snap.3048-T1
Valid prediction for Augustus_model.g15605.t1
Valid prediction for Augustus_model.g15610.t1
Valid prediction for GlimmerHMM_glimmerT_23420-T1
Valid prediction for GlimmerHMM_glimmerT_23430-T1
Valid prediction for GlimmerHMM_glimmerT_23424-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 26064, rend_intergenic: 22667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28794, rend_intergenic: 26748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68377, rend_intergenic: 64365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69788, rend_intergenic: 68385  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89699, rend_intergenic: 89636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116097, rend_intergenic: 114072  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139531, rend_intergenic: 131367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145180, rend_intergenic: 141285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157080, rend_intergenic: 154187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163425, rend_intergenic: 157309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168882, rend_intergenic: 164511  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169529, rend_intergenic: 169489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186649, rend_intergenic: 183961  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194993, rend_intergenic: 192398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 199220
-exon list size: 409


building trellis

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38.7    
38.9    
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40.6    
40.9    
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42.8    
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43.3    
43.6    
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44.0    
44.3    
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45.0    
45.3    
45.5    
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46.0    
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46.5    
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47.4    
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48.2    
48.4    
48.7    
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79.6    
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81.5    
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87.6    
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88.6    
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89.3    
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90.8    
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91.2    
91.5    
91.7    
92.0    
92.2    
92.5    
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92.9    
93.2    
93.4    
93.7    
93.9    
94.2    
94.4    
94.6    
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95.4    
95.6    
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96.1    
96.4    
96.6    
96.8    
97.1    
97.3    
97.6    
97.8    
98.1    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 26064, rend_intergenic: 22667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28794, rend_intergenic: 26748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68377, rend_intergenic: 64365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69788, rend_intergenic: 68385  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89699, rend_intergenic: 89636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116097, rend_intergenic: 114072  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139531, rend_intergenic: 131367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145180, rend_intergenic: 141285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157080, rend_intergenic: 154187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163425, rend_intergenic: 157309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168882, rend_intergenic: 164511  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169529, rend_intergenic: 169489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186649, rend_intergenic: 183961  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194993, rend_intergenic: 192398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support